AMBER Archive (2005) - By Author

Starting: Sat Jan 01 2005 - 08:25:14 CST
Ending: Sat Dec 31 2005 - 12:51:27 CST

• 'Ross Walker'
  • RE: AMBER: setting up Parallel processing (Thu May 26 2005 - 13:14:18 CDT)
  • RE: AMBER: why is snaupe.f is empty? (Thu May 26 2005 - 13:14:34 CDT)
• A D
  • Re: AMBER: problem with ssh and xleap (Fri Dec 30 2005 - 21:06:15 CST)
  • AMBER: problem with ssh and xleap (Tue Dec 27 2005 - 14:12:51 CST)
• aanzellotti_at_mail2.vcu.edu
  • Re: AMBER: generating over 16 bps of DNA in nucgen (Tue May 17 2005 - 10:57:45 CDT)
  • AMBER: segmentation problem (Thu Apr 28 2005 - 18:46:36 CDT)
  • RE: AMBER: Problem saving file in xleap (Thu Mar 17 2005 - 10:45:07 CST)
  • AMBER: Problem saving file in xleap (Tue Mar 15 2005 - 11:03:12 CST)
• Abd Ghani Abd Aziz
  • Re: AMBER: maximum number of processors (Sat May 14 2005 - 01:42:49 CDT)
• acb15885_at_uprm.edu
  • AMBER: pb_pgb test fail (Mon Jun 27 2005 - 13:17:48 CDT)
• Adrian E. Roitberg
  • Re: AMBER: No exchange among replicas in REMD! (Sun Dec 18 2005 - 17:16:22 CST)
  • Re: AMBER: langevin, GB and simulated annealing? (Mon Apr 18 2005 - 10:21:04 CDT)
  • AMBER: protonated aspartic acid (Tue Mar 29 2005 - 14:14:35 CST)
  • Re: AMBER: "personality" of Amber force field (Fri Mar 18 2005 - 15:24:50 CST)
  • Re: AMBER: Steered Molecular Dynamics with AMBER? (Wed Jan 05 2005 - 08:13:10 CST)
• Adrian Roitberg
  • Re: AMBER: Clustering - MMTSB Toolkit kclust (Wed Dec 07 2005 - 14:46:50 CST)
  • Re: AMBER: CD spectrum (Mon Nov 28 2005 - 09:10:15 CST)
  • Re: AMBER: minimization stuck problem (Sun Aug 21 2005 - 16:29:53 CDT)
• Agata Jurkiewicz
  • Re: AMBER: SHAKE error (Fri Jul 22 2005 - 17:06:49 CDT)
  • Re: AMBER: SHAKE error (Fri Jul 22 2005 - 14:12:10 CDT)
  • Re: AMBER: SHAKE error (Fri Jul 22 2005 - 12:01:16 CDT)
  • AMBER: SHAKE error (Fri Jul 22 2005 - 09:09:34 CDT)
• Aknb
  • AMBER: serial and parallel (Sun Apr 24 2005 - 06:35:37 CDT)
• Akshay Patny
  • AMBER: X Windows for LEaP on SGI (Tue Mar 08 2005 - 15:07:44 CST)
• aldo jongejan
  • Re: AMBER: Steered Molecular Dynamics with AMBER? (Wed Jan 05 2005 - 01:46:44 CST)
• Alec M. Resnick
  • AMBER: Simple 3D Molecule Visualization (Tue Oct 18 2005 - 11:29:43 CDT)
• Alessio Coi
  • AMBER: problem with xleap (Fri Jul 22 2005 - 08:47:23 CDT)
  • AMBER: MM-GBSA (Wed Mar 02 2005 - 04:00:52 CST)
• Alexander Rubinstein
  • AMBER: Error in "restrt" output file (Wed Sep 14 2005 - 16:30:49 CDT)
• Alfonso Garcia-Sosa
  • Re: AMBER: Can GB and MS work correctly together in mmpbsa? (Mon Jul 18 2005 - 14:16:21 CDT)
• alice
  • Re: Re: AMBER: bad atom type: H (Wed Jun 15 2005 - 20:35:00 CDT)
  • AMBER: bad atom type: H (Wed Jun 15 2005 - 05:53:50 CDT)
  • AMBER: How to run amber more efficiently? (Tue Jun 07 2005 - 21:59:26 CDT)
• aloks_at_mbu.iisc.ernet.in
  • AMBER: (Fri Nov 25 2005 - 06:11:01 CST)
• Amber
  • AMBER: what is wrong with my amber job or installation? (Wed Apr 13 2005 - 13:57:56 CDT)
  • AMBER: Make test error (Thu Mar 24 2005 - 15:10:53 CST)
• Amber admin
  • Re: AMBER: AMBER 8 compilation with lahey F95 ! (Mon Nov 07 2005 - 13:08:03 CST)
  • AMBER: creating a new residue (Mon Feb 28 2005 - 10:44:59 CST)
  • Re: AMBER: RE:Amber 8 with lam compilation problem (Wed Feb 23 2005 - 14:39:02 CST)
• Amber Correspondece
  • AMBER: Amber 8 and PATH buffer overflow (Thu Sep 08 2005 - 12:01:45 CDT)
• amit_at_mbu.iisc.ernet.in
  • Re: AMBER: mm_pbsa energy decomposition error (Thu Aug 25 2005 - 06:57:18 CDT)
  • AMBER: mm_pbsa energy decomposition error (Wed Aug 24 2005 - 07:06:34 CDT)
  • Re: AMBER: mm_pbsa (Sat Aug 20 2005 - 02:46:24 CDT)
  • AMBER: mm_pbsa (Thu Aug 18 2005 - 16:04:40 CDT)
  • Re: AMBER: capping (Thu Apr 28 2005 - 01:15:19 CDT)
  • AMBER: capping (Wed Apr 27 2005 - 02:30:37 CDT)
• Ananda Rama Krishnan Selvaraj
  • Re: AMBER: Cluster - input files (Mon Nov 28 2005 - 14:39:44 CST)
  • AMBER: Cluster - input files (Mon Nov 28 2005 - 04:37:22 CST)
  • AMBER: Error in MD run! (Fri Sep 02 2005 - 05:42:54 CDT)
  • Re: AMBER: Atom type :Si (Fri Jul 22 2005 - 14:45:30 CDT)
  • AMBER: Atom type :Si (Thu Jul 21 2005 - 14:02:23 CDT)
  • AMBER: doubt on the value of Pressure on MD run (Tue Jul 12 2005 - 03:21:07 CDT)
  • AMBER: how to see the box lines (Sat Jul 09 2005 - 13:10:50 CDT)
  • AMBER: how to make cluster files? (Fri Jul 01 2005 - 02:10:05 CDT)
  • Re: AMBER: Extended bonds-MD (Wed Jun 15 2005 - 07:55:41 CDT)
  • AMBER: Extended bonds-MD (Wed Jun 15 2005 - 02:02:25 CDT)
  • AMBER: Extended bonds-MD (Tue Jun 14 2005 - 11:29:29 CDT)
  • AMBER: Restrained-MD (Mon Jun 13 2005 - 18:04:14 CDT)
  • Re: RE: AMBER: problem in minimization (Thu Jun 02 2005 - 02:39:36 CDT)
  • AMBER: problem in minimization (Wed Jun 01 2005 - 03:48:46 CDT)
  • AMBER: how to make the prepin file for dimer and clusters of organic molecule in Amber7 (Fri Apr 15 2005 - 03:11:27 CDT)
  • Re: AMBER: How to fix the torsion angles during energy minimization (Fri Apr 01 2005 - 06:54:18 CST)
  • AMBER: How to fix the torsion angles during energy minimization (Fri Apr 01 2005 - 00:42:27 CST)
• Anderson Bond
  • Purchased a New Home (Mon Aug 15 2005 - 00:52:56 CDT)
• Andreas Kerzmann
  • AMBER: Sander is changing directories (Wed Jun 08 2005 - 04:39:23 CDT)
  • AMBER: Sander is changing directories (Wed Jun 08 2005 - 04:37:58 CDT)
• Andreas Svrcek-Seiler
  • Re: AMBER: My model loses its motion in MD (Thu Nov 24 2005 - 10:07:42 CST)
  • Re: AMBER: problems installing amber 7 on a RH Linux 8 machine (Fri Oct 28 2005 - 02:44:20 CDT)
  • Re: AMBER: AMBER compilation error (Fri Oct 07 2005 - 04:46:24 CDT)
  • Re: AMBER: Installation error - icc: command not found (Wed Oct 05 2005 - 04:47:31 CDT)
  • Re: AMBER: cut-offs in non-periodic simulations (Mon Oct 03 2005 - 14:15:19 CDT)
  • Re: AMBER: AMBER7 xleap problem (Thu Sep 22 2005 - 07:28:31 CDT)
  • Re: AMBER: P4 EM64T Intel Fortran Compile Problem (Fri Jul 15 2005 - 12:49:47 CDT)
  • Re: AMBER: Leap compilation issues (Mon Jul 11 2005 - 05:43:39 CDT)
  • Re: AMBER: GCC for AMBER on 64 bit machine (Thu Jun 23 2005 - 13:44:44 CDT)
  • RE: AMBER: Installation problem - wrong address (Fri Jun 17 2005 - 12:28:43 CDT)
  • RE: AMBER: Installation problem. . (Fri Jun 17 2005 - 12:12:10 CDT)
  • Re: AMBER: Installation problem. . (Thu Jun 16 2005 - 23:54:42 CDT)
  • Re: AMBER: Installation problem. . (Wed Jun 15 2005 - 07:31:46 CDT)
  • Re: AMBER: amber code (Tue May 24 2005 - 09:18:11 CDT)
  • Re: RE: AMBER: problem with gb md (Fri May 06 2005 - 04:19:00 CDT)
  • Re: AMBER: fast 1/r methods (Mon May 02 2005 - 09:18:22 CDT)
  • Re: AMBER: langevin, GB and simulated annealing - 2 (Wed Apr 20 2005 - 03:03:56 CDT)
  • Re: AMBER: About NAB (Thu Apr 14 2005 - 12:03:49 CDT)
  • Re: AMBER: GB with Langevin dynamics problem 2 (Fri Apr 08 2005 - 12:55:48 CDT)
  • Re: AMBER: GB with Langevin dynamics problem (Tue Apr 05 2005 - 12:04:08 CDT)
  • Re: AMBER: Sander minimization & dynamic question (Mon Apr 04 2005 - 07:01:32 CDT)
  • Re: AMBER: spherical boundary condition (Mon Mar 14 2005 - 12:36:06 CST)
  • Re: AMBER: XMGR (Fri Feb 18 2005 - 14:31:15 CST)
• Andrew Box
  • RE: AMBER: How to use XLEAP to link one atom in a monomer to another atom in ano (Mon Nov 21 2005 - 16:48:34 CST)
  • AMBER: DNA simulations (Sun Nov 06 2005 - 23:15:15 CST)
  • AMBER: EEL and EAMBER values (Wed Nov 02 2005 - 22:19:14 CST)
  • AMBER: (no subject) (Mon Sep 26 2005 - 23:40:51 CDT)
  • AMBER: Add constraints over time (Fri Aug 26 2005 - 00:51:49 CDT)
  • AMBER: FW: (Tue Jul 19 2005 - 21:07:44 CDT)
  • AMBER: Mol2 to prepin file conversion (Thu May 26 2005 - 19:08:22 CDT)
  • AMBER: PTRAJ $ Antechamber (Thu Mar 10 2005 - 00:47:29 CST)
  • RE: AMBER: Redhat Enterprise Linux (Tue Feb 01 2005 - 17:37:55 CST)
  • AMBER: N Metyl amino acids (Mon Jan 31 2005 - 23:14:47 CST)
  • AMBER: Converting prmtop and inpcrd files (Tue Jan 18 2005 - 17:02:02 CST)
• Andy Purkiss
  • Re: AMBER: ifort compiling problem (Wed Nov 30 2005 - 09:39:48 CST)
  • Re: AMBER: Leap handling crystallographic waters (Tue Nov 22 2005 - 08:31:07 CST)
  • Re: AMBER: Question about PDB format (Sat Nov 19 2005 - 13:19:00 CST)
  • Re: AMBER: fail of minimization in sander (Tue Jun 07 2005 - 07:17:24 CDT)
  • Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) (Fri May 06 2005 - 06:05:36 CDT)
• Angela Liu
  • Re: AMBER: Amber 8: questions about free energy perturbation (Fri Sep 16 2005 - 10:15:26 CDT)
  • Re: AMBER: Amber 8: questions about free energy perturbation (Tue Sep 13 2005 - 11:06:18 CDT)
  • Re: AMBER: Amber 8: questions about free energy perturbation (Tue Sep 13 2005 - 08:34:25 CDT)
  • Re: AMBER: Amber 8: questions about free energy perturbation (Mon Sep 12 2005 - 07:28:49 CDT)
  • RE: AMBER: Amber 8: questions about free energy perturbation (Mon Sep 12 2005 - 05:37:30 CDT)
  • Re: AMBER: Amber 8: questions about free energy perturbation (Mon Sep 12 2005 - 05:40:34 CDT)
  • AMBER: Amber 8: questions about free energy perturbation (Sun Sep 11 2005 - 19:43:41 CDT)
  • Re: AMBER: parm99.dat non-bonded parameters (Fri Aug 19 2005 - 12:44:03 CDT)
  • AMBER: parm99.dat non-bonded parameters (Thu Aug 18 2005 - 17:00:45 CDT)
  • AMBER: Amber 8: all_nucleic94.lib nucleotide geometry (Wed Aug 17 2005 - 17:42:03 CDT)
  • Re: AMBER: Amber 8: heterogeneous multiple copy LES method (Fri Jul 15 2005 - 09:16:23 CDT)
  • AMBER: Amber 8: heterogeneous multiple copy LES method (Wed Jul 13 2005 - 13:47:08 CDT)
  • AMBER: Amber 8: create topology for solvent - PBC box size problem (Wed Jul 13 2005 - 13:41:04 CDT)
  • AMBER: amber 8 leap topology file dihedral term problem (Tue Jun 28 2005 - 08:59:57 CDT)
• Angelo Pugliese
  • AMBER: Merry Xmas (Thu Dec 22 2005 - 05:43:14 CST)
  • AMBER: Atoms restrain (Mon Dec 19 2005 - 07:09:35 CST)
  • AMBER: PARM-99 (Fri Nov 25 2005 - 08:03:23 CST)
  • Re: AMBER: question about grid in ptraj (Fri Oct 07 2005 - 04:23:17 CDT)
  • AMBER: Energy decomposition parameters (Fri Jul 15 2005 - 03:57:21 CDT)
  • Re: AMBER: DNA strands separate (Wed Jul 06 2005 - 10:00:00 CDT)
  • Re: AMBER: how to average the structure along md trajectory (Wed Jul 06 2005 - 10:02:48 CDT)
  • Re: AMBER: DNA strands separate (Wed Jul 06 2005 - 09:04:36 CDT)
  • Re: AMBER: DNA strands separate (Wed Jul 06 2005 - 07:46:05 CDT)
  • Re: AMBER: Stacking energy (Fri Jul 01 2005 - 09:38:37 CDT)
  • Re: AMBER: Stacking energy (Fri Jul 01 2005 - 05:42:28 CDT)
  • AMBER: Stacking energy (Fri Jul 01 2005 - 03:32:34 CDT)
  • Re: AMBER: time and lifetime in hbond analysis (ptraj) (Tue Jun 14 2005 - 09:57:56 CDT)
  • Re: AMBER: creating pdb file.... (Tue Jun 14 2005 - 06:11:41 CDT)
  • Re: AMBER: rotating and repositioning molecules in xleap (Sun May 22 2005 - 04:37:44 CDT)
  • AMBER: Relative stability with MMPBSA (Wed May 04 2005 - 11:09:27 CDT)
• Ann Vilan Tran
  • AMBER: Solvation in trifluoroethanol (Tue Nov 29 2005 - 13:57:17 CST)
• Anna Feldman-Salit
  • AMBER: parameters for pyridoxal phosphate (Fri Oct 07 2005 - 08:46:29 CDT)
• Annette Höglund
  • AMBER: phosphorylated DNA not recognized (Thu Mar 03 2005 - 08:55:18 CST)
• Anselm Horn
  • AMBER: ptraj8: trajectory windows (Tue Feb 22 2005 - 11:16:13 CST)
• anshul_at_imtech.res.in
  • Re: AMBER: installation of amber 8 on windows (Fri Feb 18 2005 - 08:33:40 CST)
  • AMBER: installation of amber 8 on windows (Thu Feb 17 2005 - 14:17:11 CST)
  • Re: AMBER: Problem in ptraj (Wed Feb 02 2005 - 16:04:28 CST)
  • Re: AMBER: Problem in ptraj (Tue Feb 01 2005 - 16:26:48 CST)
  • AMBER: Problem in ptraj (Mon Jan 31 2005 - 16:23:30 CST)
  • Re: AMBER: Floating Exception and installation on Digital Unix. (Tue Jan 11 2005 - 09:17:32 CST)
  • AMBER: Floating Exception and installation on Digital Unix. (Sun Jan 09 2005 - 21:32:11 CST)
  • Re: AMBER: Floating Exception in sander (Fri Jan 07 2005 - 08:14:12 CST)
  • AMBER: Floating Exception in sander (Wed Jan 05 2005 - 17:26:20 CST)
• Anthony Cruz
  • AMBER: rmsd (Tue Dec 20 2005 - 13:17:51 CST)
  • AMBER: CD spectrum (Mon Nov 28 2005 - 11:58:34 CST)
  • AMBER: REMD trajectory error!!! (Fri Oct 28 2005 - 13:10:18 CDT)
  • Fwd: Re: AMBER: REMD error!!! (Fri Oct 28 2005 - 08:06:39 CDT)
  • Re: AMBER: REMD error!!! (Thu Oct 20 2005 - 14:13:20 CDT)
  • Re: AMBER: REMD error!!! (Thu Oct 20 2005 - 11:48:12 CDT)
  • Re: AMBER: REMD error!!! (Thu Oct 20 2005 - 09:45:32 CDT)
  • AMBER: REMD error!!! (Thu Oct 20 2005 - 08:53:18 CDT)
  • AMBER: Trajectory Problem (Thu Sep 22 2005 - 15:24:10 CDT)
  • Re: AMBER: REM error (Tue Sep 13 2005 - 16:36:21 CDT)
  • Re: AMBER: REM error (Tue Sep 13 2005 - 13:37:19 CDT)
  • Re: AMBER: REM error (Tue Sep 13 2005 - 07:37:13 CDT)
  • AMBER: REM error (Mon Sep 12 2005 - 19:06:05 CDT)
  • Re: AMBER: Fail to run parallel (Mon Sep 12 2005 - 08:27:50 CDT)
  • AMBER: Fail to run parallel (Mon Sep 12 2005 - 07:52:29 CDT)
  • AMBER: parralel test (Fri Sep 09 2005 - 15:41:44 CDT)
  • AMBER: amber compilation on SGI ALTIX 350 (TEST FAILD) (Fri Sep 09 2005 - 14:19:12 CDT)
  • Re: AMBER: Temperature equilibration (Mon Aug 29 2005 - 14:47:36 CDT)
  • AMBER: Temperature equilibration (Mon Aug 29 2005 - 07:44:04 CDT)
  • Re: AMBER: Replica exchange (Mon Aug 29 2005 - 07:46:52 CDT)
  • Re: AMBER: replica exchange (Fri Aug 26 2005 - 13:14:47 CDT)
  • AMBER: replica exchange (Fri Aug 26 2005 - 11:53:48 CDT)
  • AMBER: Replica exchange (Wed Aug 24 2005 - 12:57:42 CDT)
  • AMBER: essential dynamics (Wed Aug 24 2005 - 12:50:03 CDT)
  • AMBER: replica exchange (Wed Aug 10 2005 - 13:13:41 CDT)
  • Re: AMBER: sander problem (Thu Jul 07 2005 - 10:25:29 CDT)
  • AMBER: sander problem (Wed Jul 06 2005 - 18:05:44 CDT)
  • AMBER: Replica exchange (Fri Jul 01 2005 - 09:33:46 CDT)
  • AMBER: cavity volume (Fri Jul 01 2005 - 07:46:24 CDT)
  • Re: AMBER: Solvate question? (Tue Jun 07 2005 - 07:31:30 CDT)
  • AMBER: Solvents (Mon Jun 06 2005 - 11:00:07 CDT)
  • Re: AMBER: Solvate question? (Mon Jun 06 2005 - 10:59:06 CDT)
  • Re: AMBER: Compile question?? (Mon Jun 06 2005 - 08:24:40 CDT)
  • AMBER: Compile question?? (Mon Jun 06 2005 - 06:59:13 CDT)
  • AMBER: Solvate question? (Mon Jun 06 2005 - 05:30:44 CDT)
  • Re: AMBER: Protein ions? (Thu Jun 02 2005 - 11:45:34 CDT)
  • AMBER: Protein ions? (Thu Jun 02 2005 - 09:12:56 CDT)
  • Fwd: Re: AMBER: AMBER Test (Wed May 11 2005 - 10:49:38 CDT)
  • Fwd: Re: AMBER: AMBER Test (Tue May 03 2005 - 07:25:46 CDT)
  • AMBER: AMBER Test (Tue Apr 26 2005 - 05:36:27 CDT)
• Anthony Fejes
  • Re: AMBER: parm99.dat non-bonded parameters (Fri Aug 19 2005 - 13:18:36 CDT)
  • Re: AMBER: parm99.dat non-bonded parameters (Fri Aug 19 2005 - 11:35:36 CDT)
  • Re: AMBER: .dat and frcmod files (Mon Jan 10 2005 - 16:47:12 CST)
  • Re: AMBER: Steered Molecular Dynamics with AMBER? (Wed Jan 05 2005 - 10:26:05 CST)
  • AMBER: AMBER related employment (Mon Jan 03 2005 - 19:43:24 CST)
• Anton B. Guliaev
  • AMBER: Metals with Amber (Fri Oct 28 2005 - 12:09:07 CDT)
• anwar_at_cdfd.org.in
  • AMBER: floating point exception (Tue Aug 30 2005 - 21:27:47 CDT)
  • AMBER: (Mon Aug 29 2005 - 22:59:49 CDT)
  • AMBER: floating point exception (Mon Aug 29 2005 - 23:00:31 CDT)
• Arantxa Sanz
  • Re: AMBER: linit in mm-pbsa (Fri Apr 08 2005 - 04:43:22 CDT)
  • RE: AMBER: Andersen thermostat: target T? (Mon Jan 24 2005 - 04:18:05 CST)
  • AMBER: Andersen thermostat: target T? (Fri Jan 21 2005 - 13:06:01 CST)
• Arnoult, Eric [PRDFR]
  • RE: AMBER: An atom name with 4 characters is not compatible with Leap ? (Wed Jul 27 2005 - 10:59:43 CDT)
  • RE: AMBER: An atom name with 4 characters is not compatible with Leap ? (Wed Jul 27 2005 - 02:20:27 CDT)
  • RE: AMBER: why not minimize snapshots before MM/PBSA calculations (Wed Jul 27 2005 - 02:21:30 CDT)
  • AMBER: An atom name with 4 characters is not compatible with Leap ? (Fri Jul 22 2005 - 02:53:24 CDT)
• arubin_at_unmc.edu
  • AMBER: Cyclic peptide (Tue Feb 15 2005 - 15:12:28 CST)
• Ashutosh Suhas Jogalekar
  • AMBER: Zn complex parametrization question (Wed Mar 16 2005 - 15:27:38 CST)
• Asim Okur
  • Re: AMBER: maximum number of processors (Thu May 12 2005 - 10:41:25 CDT)
  • Re: AMBER: combine mdcrd using ptraj (Thu Apr 07 2005 - 00:17:57 CDT)
  • Re: AMBER: force constant Unit used in TMD (Mon Apr 04 2005 - 12:36:08 CDT)
  • Re:AMBER: "personality" of Amber force field (Fri Mar 18 2005 - 15:01:19 CST)
  • Re: AMBER: Trajectory problems (Thu Mar 17 2005 - 17:14:28 CST)
  • Re: AMBER: sander failure (Thu Jan 20 2005 - 16:50:25 CST)
• Atilio Anzellotti
  • AMBER: Message in .out file (Tue May 17 2005 - 07:31:36 CDT)
• Atro Tossavainen
  • Re: AMBER: Problem in running AMBER 7 in solaris ! (Fri Dec 02 2005 - 06:14:42 CST)
  • Re: AMBER: Problems with protonate on Linux (Wed Apr 06 2005 - 01:46:34 CDT)
  • AMBER: Problems with protonate on Linux (Fri Apr 01 2005 - 07:09:32 CST)
  • AMBER: AMBER under MOSIX? (Thu Mar 31 2005 - 05:47:47 CST)
  • Re: AMBER: Amber8 Parallel installation troubles (Wed Mar 23 2005 - 01:43:18 CST)
  • Re: AMBER: Amber8 Solaris installation failure (Tue Feb 22 2005 - 14:19:31 CST)
• Atsutoshi Okabe
  • AMBER: About WHAM program (Sat Nov 05 2005 - 22:16:43 CST)
  • AMBER: About WHAM program (Tue Nov 01 2005 - 21:29:14 CST)
• Austin B. Yongye
  • Re: AMBER: comparing md trajectories (Wed Aug 10 2005 - 16:16:08 CDT)
  • Re: AMBER: RESP charges - multiple conformations (Tue Apr 19 2005 - 07:43:45 CDT)
  • AMBER: RESP charges - multiple conformations (Mon Apr 18 2005 - 21:54:20 CDT)
  • Re: AMBER: Antechamber -reorders atom sequence (Fri Apr 15 2005 - 15:12:40 CDT)
  • AMBER: Antechamber -reorders atom sequence (Thu Apr 14 2005 - 07:05:09 CDT)
  • RE: AMBER: Pyranose pucker parameters (Sun Feb 27 2005 - 21:08:52 CST)
  • AMBER: Pyranose pucker parameters (Fri Feb 25 2005 - 23:10:06 CST)
  • AMBER: (Fri Feb 25 2005 - 15:43:56 CST)
  • Re: AMBER: Moil view trajectory clusters (Thu Feb 17 2005 - 15:31:37 CST)
  • AMBER: Moil view trajectory clusters (Thu Feb 17 2005 - 11:36:15 CST)
• ayongye_at_chem.uga.edu
  • AMBER: comparing md trajectories (Mon Jul 18 2005 - 20:12:15 CDT)
• Azira Muhamad
  • AMBER: Problem with restart file (Thu Jan 13 2005 - 01:45:30 CST)
• B
  • AMBER:idecomp (Thu Jan 27 2005 - 05:22:37 CST)
• B $BIp;V
  • Re:AMBER: MD simulation on a protein solvated by a combination of some water mod (Thu Jul 14 2005 - 04:56:39 CDT)
  • AMBER: MD simulation on a protein solvated by a combination of some water models ? (Mon Jul 11 2005 - 23:10:12 CDT)
• Barbault Florent
  • AMBER: installation on a dual core (Fri Dec 16 2005 - 08:00:08 CST)
  • Re: AMBER: Will Amber 9 available? (Mon Nov 21 2005 - 04:25:04 CST)
• Beale, John
  • AMBER: dihedral driver? (Tue Feb 22 2005 - 10:26:26 CST)
  • AMBER: XMGR (Fri Feb 18 2005 - 12:20:44 CST)
  • AMBER: moil-view (Thu Feb 17 2005 - 09:56:30 CST)
  • AMBER: (Wed Feb 16 2005 - 07:42:26 CST)
  • AMBER: Convert to Pdb (Wed Feb 09 2005 - 13:03:27 CST)
  • AMBER: Linux Enterprise (Tue Feb 08 2005 - 13:39:54 CST)
  • AMBER: Minimization (Tue Feb 08 2005 - 13:30:52 CST)
  • RE: AMBER: Redhat Enterprise Linux (Wed Feb 02 2005 - 12:01:53 CST)
  • AMBER: Redhat Enterprise Linux (Tue Feb 01 2005 - 11:49:20 CST)
• Ben-Zhuo Lu
  • AMBER: using position restraints in target MD? (Fri Oct 21 2005 - 13:58:05 CDT)
• Benjamin Juhl
  • AMBER: Question on makeing up of missing atoms (Fri Dec 09 2005 - 06:30:57 CST)
  • AMBER: disulfide bonds by "bond" or "edit -> draw" ? (Wed Aug 31 2005 - 11:23:45 CDT)
• Bill Ross
  • Re: AMBER: ambpdb TER problems (Mon Dec 26 2005 - 15:27:07 CST)
  • Re: AMBER: MD problems/shake (Mon Dec 19 2005 - 17:54:01 CST)
  • Re: AMBER: MD problems/shake (Mon Dec 19 2005 - 17:50:33 CST)
  • Re: AMBER: MD problems/shake (Mon Dec 19 2005 - 17:14:10 CST)
  • Re: AMBER: MD problems/shake (Mon Dec 19 2005 - 14:59:04 CST)
  • Re: AMBER: Adding/recognizing calcium atoms (Wed Dec 07 2005 - 15:32:05 CST)
  • Re: AMBER: Using OPLS atom types (Sat Dec 03 2005 - 12:15:53 CST)
  • Re: AMBER: constant pressure vs. constant volume heating (Tue Nov 29 2005 - 13:51:12 CST)
  • Re: AMBER: Cluster - input files (Mon Nov 28 2005 - 15:51:04 CST)
  • Re: AMBER: gaff sugar residue instability (Thu Nov 24 2005 - 12:48:02 CST)
  • Re: AMBER: gaff sugar residue instability (Thu Nov 24 2005 - 12:45:16 CST)
  • Re: AMBER: Using OPLS atom types (Tue Nov 22 2005 - 11:44:16 CST)
  • Re: AMBER: using periodic boundary conditions to create infinite double helix (Wed Nov 16 2005 - 18:34:53 CST)
  • Re: AMBER: anal and periodic boundary conditions (Wed Nov 16 2005 - 11:32:57 CST)
  • Re: AMBER: restart coordinate file (Thu Nov 10 2005 - 09:42:53 CST)
  • Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list (Wed Nov 09 2005 - 19:40:41 CST)
  • RE: AMBER: vdw of h atoms (Fri Oct 28 2005 - 19:21:56 CDT)
  • Re: AMBER: vdw of h atoms (Fri Oct 28 2005 - 17:13:59 CDT)
  • Re: AMBER: Metals with Amber (Fri Oct 28 2005 - 15:56:50 CDT)
  • Re: AMBER: seg fault error in resp (Thu Oct 27 2005 - 13:40:47 CDT)
  • Re: AMBER: seg fault error in resp (Wed Oct 26 2005 - 11:35:38 CDT)
  • Re: AMBER: Is MM-PBSA doable for transition metals ? (Mon Oct 24 2005 - 12:10:44 CDT)
  • Re: AMBER: Equillibration run (Fri Sep 09 2005 - 09:30:40 CDT)
  • RE: AMBER: Amber 8 and PATH buffer overflow (Thu Sep 08 2005 - 12:57:42 CDT)
  • Re: AMBER: carnal problem (Thu Sep 08 2005 - 10:51:34 CDT)
  • Re: AMBER: STARTING WHERE I LEFT OFF (Sat Sep 03 2005 - 17:55:19 CDT)
  • Re: AMBER: STARTING WHERE I LEFT OFF (Sat Sep 03 2005 - 13:12:40 CDT)
  • Re: AMBER: STARTING WHERE I LEFT OFF (Sat Sep 03 2005 - 12:36:23 CDT)
  • Re: AMBER: Equilibration MD (Sat Sep 03 2005 - 11:53:17 CDT)
  • Re: AMBER: fixing protein for minimisation of solvent (Sat Sep 03 2005 - 11:49:18 CDT)
  • RE: AMBER: Interpreting Amber8 Benchmark Results (Wed Aug 31 2005 - 16:29:58 CDT)
  • RE: AMBER: Interpreting Amber8 Benchmark Results (Wed Aug 31 2005 - 15:44:55 CDT)
  • Re: AMBER: disulfide bonds by "bond" or "edit -> draw" ? (Wed Aug 31 2005 - 11:57:23 CDT)
  • Re: AMBER: Amber 8: all_nucleic94.lib nucleotide geometry (Wed Aug 17 2005 - 18:04:49 CDT)
  • Re: AMBER: Tutorial question and some more... (Tue Aug 09 2005 - 13:30:46 CDT)
  • Re: AMBER: bond breaking/ energetic ion (Wed Aug 03 2005 - 12:41:36 CDT)
  • Re: AMBER: lib file for nonstandard residue (Thu Jul 14 2005 - 17:20:25 CDT)
  • Re: AMBER: lib file for nonstandard residue (Thu Jul 14 2005 - 14:37:01 CDT)
  • Re: AMBER: lib file for nonstandard residue (Thu Jul 14 2005 - 14:08:03 CDT)
  • Re: AMBER: Leap compilation issues (Mon Jul 11 2005 - 20:34:35 CDT)
  • Re: AMBER: Leap compilation issues (Sun Jul 10 2005 - 21:11:43 CDT)
  • Re: AMBER: building nucleic acids (Fri Jul 08 2005 - 14:05:15 CDT)
  • Re: AMBER: nucgen and nukit (Tue Jul 05 2005 - 11:33:04 CDT)
  • Re: AMBER: question about Carnal (Wed Jun 22 2005 - 15:51:34 CDT)
  • RE: AMBER: vdw for terminal phosphate (Mon Jun 13 2005 - 15:22:47 CDT)
  • Re: AMBER: vdw for terminal phosphate (Fri Jun 10 2005 - 13:10:32 CDT)
  • Re: AMBER: nucgen problem (Tue Jun 07 2005 - 14:27:14 CDT)
  • Re: AMBER: AMBER frcmod+off input vs. prep input (Tue Jun 07 2005 - 12:58:06 CDT)
  • Re: AMBER: nucgen problem (Tue Jun 07 2005 - 11:47:42 CDT)
  • Re: AMBER: segmentation fault in sander (Tue Jun 07 2005 - 11:35:27 CDT)
  • Re: AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 19:03:38 CDT)
  • Re: AMBER: segmentation fault in sander (Mon Jun 06 2005 - 17:18:45 CDT)
  • Re: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 12:58:54 CDT)
  • Re: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 09:34:39 CDT)
  • Re: AMBER: fail of minimization in sander (Sun Jun 05 2005 - 22:50:48 CDT)
  • Re: AMBER: Is the MD simulation normal (Tue May 31 2005 - 22:41:42 CDT)
  • RE: AMBER:Sander errors: Unit 6 Error on OPEN: mdout (Tue May 31 2005 - 13:42:50 CDT)
  • Re: AMBER: STOP 0 (Tue May 31 2005 - 12:43:32 CDT)
  • Re: AMBER: density profiles in ptraj or carnal (Tue May 31 2005 - 11:13:28 CDT)
  • Re: AMBER: density profiles in ptraj or carnal (Mon May 30 2005 - 12:00:08 CDT)
  • Re: AMBER: Is the MD simulation normal (Mon May 30 2005 - 11:49:32 CDT)
  • RE: AMBER: Is the MD simulation normal (Sun May 29 2005 - 12:04:01 CDT)
  • Re: AMBER: Is the MD simulation normal (Sun May 29 2005 - 10:33:13 CDT)
  • Re: AMBER: Is the MD simulation normal (Sat May 28 2005 - 12:00:42 CDT)
  • Re: AMBER: Is the MD simulation normal (Fri May 27 2005 - 13:14:30 CDT)
  • Re: AMBER: dissolving micelle structure in water.. amber7 (Thu May 26 2005 - 11:50:23 CDT)
  • Re: AMBER: hbond analysis in ptaj/carnal (Thu May 26 2005 - 11:44:13 CDT)
  • Re: AMBER: Unexpected stop of Sander run (Sun May 22 2005 - 15:18:16 CDT)
  • Re: AMBER: rotating and repositioning molecules in xleap (Sun May 22 2005 - 10:36:16 CDT)
  • Re: AMBER: crashing xleap (Fri May 20 2005 - 14:55:15 CDT)
  • RE: AMBER: read pdb back to xleap after solvation of chloroform (Thu May 19 2005 - 22:56:58 CDT)
  • RE: AMBER: read pdb back to xleap after solvation of chloroform (Thu May 19 2005 - 21:16:22 CDT)
  • Re: AMBER: Can we load prmtop and inpcrd files into xleap? (Wed May 18 2005 - 23:49:04 CDT)
  • Re: AMBER: how to reduce box size and delete excess solvent (Sun May 15 2005 - 14:50:01 CDT)
  • Re: AMBER: Calculating of radius of gyration in Carnal (Sat May 14 2005 - 17:26:43 CDT)
  • Re: AMBER: AMBER8 Build on Linux x64 running Opterons (Thu May 12 2005 - 15:08:34 CDT)
  • Re: AMBER: How can I read parm99.dat file? (Fri May 06 2005 - 15:08:59 CDT)
  • Re: AMBER: How can I read parm99.dat file? (Wed May 04 2005 - 19:12:08 CDT)
  • Re: AMBER: false bond created upon coordinate retrieval (Thu Apr 28 2005 - 17:00:38 CDT)
  • Re: AMBER: capping (Thu Apr 28 2005 - 01:41:48 CDT)
  • Re: AMBER: capping (Wed Apr 27 2005 - 16:00:50 CDT)
  • Re: AMBER: Calculate vdw parameters for alkaline earth metal ions (Fri Apr 22 2005 - 17:48:15 CDT)
  • Re: AMBER: carnal problem (Fri Apr 15 2005 - 14:20:03 CDT)
  • Re: AMBER: carnal problem (Fri Apr 15 2005 - 13:42:16 CDT)
  • Re: AMBER: carnal problem (Fri Apr 15 2005 - 12:32:02 CDT)
  • Re: AMBER: periodic boundaries and repeating structure (Thu Apr 14 2005 - 13:13:48 CDT)
  • Re: AMBER: ibelly not working (Tue Apr 12 2005 - 13:11:28 CDT)
  • Re: AMBER: peptide side chain modification with LEAP (Tue Apr 12 2005 - 11:22:40 CDT)
  • Re: AMBER: problems with "protonate" (Tue Apr 12 2005 - 11:14:27 CDT)
  • Re: Re: AMBER: Fail to load the trajectory file. (Mon Apr 11 2005 - 20:11:19 CDT)
  • Re: AMBER: Fail to load the trajectory file. (Mon Apr 11 2005 - 19:41:52 CDT)
  • Re: AMBER: problems with "protonate" (Mon Apr 11 2005 - 17:33:17 CDT)
  • Re: AMBER: breaking symmetry in minimization (Mon Apr 11 2005 - 17:25:25 CDT)
  • Re: AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters (Tue Apr 05 2005 - 11:26:34 CDT)
  • Re: AMBER: GB dynamics (Fri Apr 01 2005 - 15:55:07 CST)
  • RE: AMBER: wierd behavior of addions (Tue Mar 22 2005 - 15:23:52 CST)
  • Re: AMBER: periodicity problem (Wed Mar 16 2005 - 16:23:03 CST)
  • Re: AMBER: Question about radial command in ptraj (Mon Mar 14 2005 - 15:09:08 CST)
  • Re: AMBER: Question about radial command in ptraj (Mon Mar 14 2005 - 13:48:17 CST)
  • Re: AMBER: gyration radius (Sun Mar 13 2005 - 13:36:15 CST)
  • Re: Re :AMBER: Holes in water (Sat Mar 12 2005 - 13:15:43 CST)
  • Re: Re :AMBER: Holes in water (Sat Mar 12 2005 - 12:13:06 CST)
  • Re: Re :AMBER: Holes in water (Fri Mar 11 2005 - 09:59:03 CST)
  • Re: AMBER: Re: inconsistent ordering in an improper dihedral of TRP (Fri Mar 11 2005 - 09:46:40 CST)
  • Re: AMBER: PTRAJ $ Antechamber (Thu Mar 10 2005 - 11:22:39 CST)
  • Re: AMBER: vlimit in heating (Wed Mar 09 2005 - 09:44:06 CST)
  • Re: AMBER: amber on sgi (Wed Mar 09 2005 - 09:35:21 CST)
  • Re: AMBER: heating (Tue Mar 08 2005 - 16:55:47 CST)
  • Re: AMBER: radii "leap" from which file (Tue Mar 08 2005 - 15:43:18 CST)
  • RE: AMBER: Amber8 Solaris installation failure (Tue Feb 22 2005 - 18:08:37 CST)
  • Re: AMBER: Formatting Questions (Tue Feb 22 2005 - 18:03:26 CST)
  • Re: AMBER: leap saveamberparm chain types response (Thu Feb 17 2005 - 19:15:20 CST)
  • Re: AMBER: Why I couldnt used carnal for analyzed RMSD ? (Wed Feb 16 2005 - 12:19:30 CST)
  • Re: AMBER: inconsistent ordering in an improper dihedral of TRP (Fri Feb 11 2005 - 19:56:10 CST)
  • RE: AMBER: minimize a ptraj average pdb structure (Wed Feb 09 2005 - 13:39:27 CST)
  • Re: AMBER: leap bond angle building (Tue Feb 08 2005 - 18:00:12 CST)
  • Re: AMBER: problem in minimization (Tue Feb 08 2005 - 16:16:47 CST)
  • Re: AMBER: problem in minimization (Tue Feb 08 2005 - 14:16:18 CST)
  • Re: AMBER: Creating an input file for GRASP using AMBER 8 (Mon Feb 07 2005 - 13:40:33 CST)
  • Re: AMBER: doubts with a new aminoacid (Tue Feb 01 2005 - 18:36:38 CST)
  • Re: AMBER: Carnal in Amber8 (Tue Feb 01 2005 - 13:57:19 CST)
  • Re: AMBER: Carnal in Amber8 (Tue Feb 01 2005 - 13:47:15 CST)
  • Re: AMBER: Problems with xLEaP (Fri Jan 28 2005 - 16:26:12 CST)
  • Re: AMBER: carnal - water-mediated HBond (Sat Jan 22 2005 - 22:49:09 CST)
  • Re: AMBER: Converting prmtop and inpcrd files (Tue Jan 18 2005 - 17:43:04 CST)
  • Re: AMBER: amber8 parallel sander (Wed Jan 12 2005 - 14:12:18 CST)
  • Re: AMBER: the DNA conformation after engery minimization using NMODE (Mon Jan 10 2005 - 21:56:25 CST)
  • Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied (Tue Jan 04 2005 - 12:07:49 CST)
• Bing Liu
  • AMBER: Sander.LES questions (Tue Dec 20 2005 - 08:51:09 CST)
• Bing Xiong
  • AMBER: nmode minimization and normal mode calculation (Tue Aug 30 2005 - 08:53:11 CDT)
• Biswaroop Mukherjee
  • AMBER: Argon Box (Thu Jun 02 2005 - 03:44:46 CDT)
• blakrose_at_gazeta.pl
  • Re: AMBER: MD problems/shake (Tue Dec 20 2005 - 17:17:45 CST)
  • Re: AMBER: MD problems/shake-many thanks (Tue Dec 20 2005 - 17:04:24 CST)
  • Re: AMBER: Ligand problem (Mon Dec 19 2005 - 19:02:54 CST)
  • Re: AMBER: MD problems/shake (Mon Dec 19 2005 - 18:07:44 CST)
  • Re: AMBER: MD problems/shake (Mon Dec 19 2005 - 18:03:08 CST)
  • Re: AMBER: MD problems/shake (Mon Dec 19 2005 - 17:44:59 CST)
  • Re: AMBER: MD problems/shake (Mon Dec 19 2005 - 17:33:12 CST)
  • Re: AMBER: MD problems/shake (Mon Dec 19 2005 - 16:45:43 CST)
  • AMBER: MD problems/shake (Mon Dec 19 2005 - 14:34:52 CST)
  • AMBER: MD problems (SHAKE) (Mon Dec 19 2005 - 06:49:41 CST)
  • Re: AMBER: in vacuo? (Wed Aug 31 2005 - 04:44:00 CDT)
  • AMBER: minimization (Fri Aug 26 2005 - 07:20:25 CDT)
  • AMBER: minimization stuck problem (Mon Aug 22 2005 - 10:17:29 CDT)
  • Re: AMBER: minimization stuck problem (Sat Aug 20 2005 - 16:11:54 CDT)
  • AMBER: minimization stuck problem (Sat Aug 20 2005 - 07:32:31 CDT)
  • AMBER: minimization stuck problem (Sat Aug 20 2005 - 06:46:07 CDT)
  • AMBER: solvent problem (Thu Aug 11 2005 - 02:14:17 CDT)
  • Re: AMBER: Tutorial question and some more... (Tue Aug 09 2005 - 16:00:20 CDT)
  • AMBER: Tutorial question and some more... (Tue Aug 09 2005 - 01:49:45 CDT)
  • AMBER: strange minimalization output (Tue Aug 02 2005 - 09:56:38 CDT)
  • AMBER: [FWD] water minimalization problems (Wed Jul 27 2005 - 10:46:47 CDT)
• bmbbjm_at_bmb.leeds.ac.uk
  • Re: AMBER: Will Amber 9 available? (Mon Nov 21 2005 - 03:54:45 CST)
• Bogos Agianian
  • AMBER: Sample more conformational space (Wed Mar 02 2005 - 06:52:49 CST)
  • Re: AMBER: Joining residues/units (Thu Feb 24 2005 - 15:22:07 CST)
  • AMBER: Joining residues/units (Thu Feb 24 2005 - 08:58:55 CST)
• Brandon Tefft
  • AMBER: External Electric Field (Tue Feb 01 2005 - 15:30:22 CST)
• Brent Krueger
  • Re: AMBER: Cyclohexane solvent Box (Mon Oct 17 2005 - 09:59:44 CDT)
  • Re: AMBER: Could not open file (Melb.mdcrd) with mode (r) (Tue Sep 20 2005 - 19:13:32 CDT)
  • AMBER: gaff.dat typo (Wed Jun 01 2005 - 20:35:58 CDT)
  • AMBER: fast 1/r methods (Mon May 02 2005 - 06:51:56 CDT)
  • AMBER: Rep Exch. suggestion (Mon Apr 18 2005 - 06:56:33 CDT)
  • Re: AMBER: size of solventbox (Wed Feb 23 2005 - 14:54:35 CST)
• bybaker_at_itsa.ucsf.edu
  • Re: AMBER: antechamber problem (Wed Dec 21 2005 - 23:39:24 CST)
  • AMBER: Re: Ligand problem (Tue Dec 20 2005 - 12:50:03 CST)
  • AMBER: Ligand problem (Mon Dec 19 2005 - 18:40:22 CST)
  • Re: AMBER: antechamber problem (Wed Sep 21 2005 - 19:55:45 CDT)
  • AMBER: antechamber problem (Tue Sep 20 2005 - 17:20:59 CDT)
  • AMBER: solvate water box (Thu Apr 14 2005 - 01:42:21 CDT)
  • AMBER: frcmod.mod_phipsi.2 (Tue Mar 15 2005 - 14:04:31 CST)
  • Re: AMBER: The pressure (Wed Mar 09 2005 - 00:38:14 CST)
  • AMBER: The pressure (Tue Mar 08 2005 - 19:54:44 CST)
• bzlu_at_ucsd.edu
  • AMBER: can I setup a simulation with restrain the COM of a group to a reference structure? (Sun Aug 28 2005 - 15:32:33 CDT)
• C Balasubramanian
  • AMBER: average struct without solvent (Mon Nov 21 2005 - 07:51:26 CST)
  • AMBER: calculating end-end distance (Tue Nov 15 2005 - 04:24:21 CST)
• C J Kenneth Tan -- OptimaNumerics
  • Re: AMBER: maximum number of processors (Sat May 14 2005 - 09:57:22 CDT)
• Cai, Yufeng
  • AMBER: sander free energy calculation (Tue Jan 11 2005 - 13:47:03 CST)
• cailliez
  • AMBER: distance between images (Wed Jan 05 2005 - 04:34:46 CST)
• Caleb S Howe (cshowe_at_Princeton.EDU)
  • AMBER: Division by zero in sander (Thu Jul 28 2005 - 09:57:00 CDT)
• Cameron Mura
  • AMBER: solvateOct method (Wed Feb 23 2005 - 20:26:19 CST)
• caoch_at_cherry.bio.titech.ac.jp
  • Re: AMBER: Making movie from AMBER trajectory (Mon Nov 07 2005 - 20:09:16 CST)
  • Re: AMBER: fedora installation problem (Thu Nov 03 2005 - 07:17:32 CST)
  • AMBER: umbrella sampling output question (Mon Sep 12 2005 - 02:50:32 CDT)
  • AMBER: nonbond_list question . (Fri Jun 17 2005 - 20:38:27 CDT)
  • AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? (Sat May 14 2005 - 12:17:17 CDT)
• Carlos Jaime
  • AMBER: RESP: Question (Mon Dec 05 2005 - 11:43:16 CST)
  • Re: AMBER: ptraj for RDF calculations (Mon Feb 21 2005 - 03:11:22 CST)
• Carlos P. Sosa
  • Re: AMBER: amber8 parallel sander (Fri Sep 23 2005 - 07:02:26 CDT)
• Carlos Simmerling
  • Re: AMBER: Sander.LES questions (Tue Dec 20 2005 - 09:07:12 CST)
  • Re: AMBER: No exchange among replicas in REMD! (Mon Dec 19 2005 - 10:35:30 CST)
  • Re: AMBER: aniso and iso (Mon Dec 19 2005 - 06:26:37 CST)
  • Re: AMBER: No exchange among replicas in REMD! (Sun Dec 18 2005 - 20:23:14 CST)
  • Re: AMBER: No exchange among replicas in REMD! (Sun Dec 18 2005 - 20:22:48 CST)
  • Re: AMBER: No exchange among replicas in REMD! (Sun Dec 18 2005 - 16:27:25 CST)
  • Re: AMBER: No exchange among replicas in REMD! (Sun Dec 18 2005 - 16:26:42 CST)
  • Re: AMBER: distance restraints (Sat Dec 17 2005 - 17:08:28 CST)
  • Re: AMBER: parallel AMBER on cluster (Thu Dec 15 2005 - 12:55:55 CST)
  • Re: AMBER: parameters for fluorine atom (Thu Dec 15 2005 - 06:47:20 CST)
  • Re: AMBER: about antechamber(amber8) (Thu Dec 15 2005 - 06:45:59 CST)
  • Re: AMBER: E of amber calculations (Thu Dec 15 2005 - 06:30:08 CST)
  • Re: AMBER: Question on makeing up of missing atoms (Fri Dec 09 2005 - 06:57:06 CST)
  • Re: AMBER: RMSD Calculations (Mon Dec 05 2005 - 10:56:36 CST)
  • Re: AMBER: RMSD Calculations (Mon Dec 05 2005 - 10:00:23 CST)
  • Re: AMBER: Replica-Exchange MD from AMBER8! (Sat Dec 03 2005 - 15:11:07 CST)
  • Re: AMBER: Replica-Exchange MD from AMBER8! (Fri Dec 02 2005 - 16:49:25 CST)
  • Re: AMBER: Mg2+ issues of using MM-PB/GBSA (Thu Dec 01 2005 - 13:26:11 CST)
  • Re: AMBER: regarding ambpdb (Thu Dec 01 2005 - 07:57:39 CST)
  • Re: AMBER: Targeted MD (Wed Nov 30 2005 - 11:51:47 CST)
  • Re: AMBER: Comparing EELEC from amber and that calculated in the trivial fashion. (Mon Nov 28 2005 - 06:41:30 CST)
  • Re: AMBER: PARM-99 (Fri Nov 25 2005 - 10:36:45 CST)
  • Re: AMBER: temprature and restraint in constant volumm MD (Mon Nov 21 2005 - 07:00:08 CST)
  • Re: AMBER: Quantifying DNA perterbation (Wed Nov 16 2005 - 05:08:41 CST)
  • Re: AMBER: restart coordinate file (Thu Nov 10 2005 - 09:31:18 CST)
  • Re: AMBER: Making movie from AMBER trajectory (Tue Nov 08 2005 - 06:44:38 CST)
  • Re: AMBER: Making movie from AMBER trajectory (Mon Nov 07 2005 - 12:28:20 CST)
  • Re: AMBER: Making movie from AMBER trajectory (Mon Nov 07 2005 - 11:45:27 CST)
  • Re: AMBER: Making movie from AMBER trajectory (Mon Nov 07 2005 - 10:28:26 CST)
  • Re: AMBER: How to generate a RMSd-residue number graph using AMBER8 ptraj? (Thu Nov 03 2005 - 19:31:39 CST)
  • Re: AMBER: REM difficulties (Thu Nov 03 2005 - 13:41:05 CST)
  • Re: AMBER: REM difficulties (Thu Nov 03 2005 - 12:38:23 CST)
  • Re: AMBER: GBSA simulation problem (Mon Oct 31 2005 - 06:25:22 CST)
  • Re: Fwd: Re: AMBER: REMD error!!! (Fri Oct 28 2005 - 09:38:48 CDT)
  • Re: AMBER: REMD trajectory error!!! (Fri Oct 28 2005 - 12:06:44 CDT)
  • Re: AMBER: restart file and crd file (Thu Oct 27 2005 - 15:03:20 CDT)
  • Re: AMBER: restart file and crd file (Thu Oct 27 2005 - 14:03:13 CDT)
  • Re: AMBER: restart file and crd file (Thu Oct 27 2005 - 11:18:18 CDT)
  • Re: AMBER: Increase the runtime of Amber benchmarks (Wed Oct 26 2005 - 06:30:37 CDT)
  • Re: AMBER: Targeted MD (Thu Oct 20 2005 - 13:31:21 CDT)
  • Re: AMBER: REMD error!!! (Thu Oct 20 2005 - 12:30:13 CDT)
  • Re: AMBER: REMD error!!! (Thu Oct 20 2005 - 11:28:15 CDT)
  • Re: AMBER: REMD error!!! (Thu Oct 20 2005 - 11:14:25 CDT)
  • Re: AMBER: REMD error!!! (Thu Oct 20 2005 - 10:00:22 CDT)
  • Re: AMBER: REMD error!!! (Thu Oct 20 2005 - 08:35:13 CDT)
  • Re: AMBER: REMD error!!! (Thu Oct 20 2005 - 07:05:41 CDT)
  • Re: AMBER: Neutral C-terminal residue (Wed Oct 19 2005 - 06:40:10 CDT)
  • Re: AMBER: Question about NVE simulation. (Tue Oct 18 2005 - 15:23:02 CDT)
  • Re: AMBER: Question about NVE simulation. (Tue Oct 18 2005 - 07:02:39 CDT)
  • Re: AMBER: Free energy for L and D amino acids (Sun Oct 16 2005 - 11:05:03 CDT)
  • Re: AMBER: problem with temperature weights (Sat Oct 08 2005 - 06:03:41 CDT)
  • Re: AMBER: problem with temperature weights (Fri Oct 07 2005 - 11:55:12 CDT)
  • Re: AMBER: question temperature coupling tautp value for RNA (Tue Oct 04 2005 - 07:42:07 CDT)
  • Re: FW: AMBER: number of processors (Thu Sep 29 2005 - 16:44:26 CDT)
  • Re: AMBER: number of processors (Wed Sep 28 2005 - 13:01:04 CDT)
  • Re: AMBER: (no subject) (Tue Sep 27 2005 - 06:06:16 CDT)
  • Re: AMBER: amber8 parallel sander (Thu Sep 22 2005 - 17:25:07 CDT)
  • Re: AMBER: D-enantiomers (Thu Sep 22 2005 - 06:35:06 CDT)
  • Re: AMBER: How to split LES trajectory using TRAJ (Mon Sep 19 2005 - 12:40:47 CDT)
  • Re: AMBER: about the %occupied of hydrogen bond (Mon Sep 19 2005 - 09:28:19 CDT)
  • Re: AMBER: about the %occupied of hydrogen bond (Mon Sep 19 2005 - 08:04:14 CDT)
  • Re: AMBER: using SALTCON for human cell cytoplasm (Sun Sep 18 2005 - 12:11:29 CDT)
  • Re: AMBER: about the %occupied of hydrogen bond (Fri Sep 16 2005 - 09:49:04 CDT)
  • Re: AMBER: sander prob (Fri Sep 16 2005 - 06:03:03 CDT)
  • Re: AMBER: REM error (Tue Sep 13 2005 - 12:40:20 CDT)
  • Re: AMBER: REM error (Tue Sep 13 2005 - 06:25:11 CDT)
  • Re: AMBER: mm_pbsa example number 3 (Sun Sep 11 2005 - 08:12:17 CDT)
  • Re: AMBER: mm_pbsa example number 3 (Fri Sep 09 2005 - 06:19:59 CDT)
  • Re: AMBER: Equillibration run (Fri Sep 09 2005 - 06:16:55 CDT)
  • Re: AMBER: STARTING WHERE I LEFT OFF (Sat Sep 03 2005 - 13:28:27 CDT)
  • Re: AMBER: STARTING WHERE I LEFT OFF (Sat Sep 03 2005 - 12:58:29 CDT)
  • Re: AMBER: addles question (Fri Sep 02 2005 - 14:07:30 CDT)
  • Re: AMBER: Replica exchange (Sun Aug 28 2005 - 08:16:46 CDT)
  • Re: AMBER: replica exchange (Fri Aug 26 2005 - 10:16:51 CDT)
  • Re: AMBER: Restraints (Mon Aug 22 2005 - 07:12:26 CDT)
  • Re: AMBER: minimization stuck problem (Sat Aug 20 2005 - 07:10:45 CDT)
  • Re: AMBER: shake (Fri Aug 19 2005 - 11:45:16 CDT)
  • Re: AMBER: amber8installation (Fri Aug 19 2005 - 07:13:24 CDT)
  • Re: AMBER: is calculated B-factors always smaller than experimental ones? (Sun Aug 07 2005 - 10:23:42 CDT)
  • Re: AMBER: about salt bridges (Fri Aug 05 2005 - 06:53:06 CDT)
  • Re: AMBER: a trivial question (Thu Aug 04 2005 - 06:28:36 CDT)
  • Re: AMBER: temperature keep increasing in high temp. (Fri Jul 29 2005 - 19:28:42 CDT)
  • Re: AMBER: dihedral term in prmtop file (Thu Jul 28 2005 - 09:59:36 CDT)
  • Re: AMBER: Minimized structure (Thu Jul 28 2005 - 05:53:45 CDT)
  • Re: AMBER: Thermodynamic Integration for conformational changes? (Tue Jul 26 2005 - 13:02:57 CDT)
  • Re: AMBER: SHAKE error (Fri Jul 22 2005 - 14:26:36 CDT)
  • Re: AMBER: SHAKE error (Fri Jul 22 2005 - 12:24:46 CDT)
  • Re: AMBER: SHAKE error (Fri Jul 22 2005 - 09:56:53 CDT)
  • Re: AMBER: comparing md trajectories (Tue Jul 19 2005 - 07:58:44 CDT)
  • Re: AMBER: Amber 8: heterogeneous multiple copy LES method (Thu Jul 14 2005 - 16:17:07 CDT)
  • Re: AMBER: pdb files from traj file (Wed Jul 13 2005 - 16:16:52 CDT)
  • Re: AMBER: question replica exchange acceptance ratio (Tue Jul 12 2005 - 18:43:01 CDT)
  • Re: AMBER: question replica exchange acceptance ratio (Tue Jul 12 2005 - 16:42:55 CDT)
  • Re: AMBER: doubt on the value of Pressure on MD run (Tue Jul 12 2005 - 06:07:08 CDT)
  • Re: AMBER: infinite DNA (Fri Jul 08 2005 - 18:33:59 CDT)
  • Re: AMBER: Replica Exchange (Thu Jul 07 2005 - 08:43:17 CDT)
  • Re: AMBER: restart file (Tue Jul 05 2005 - 16:22:16 CDT)
  • Re: AMBER: restart file (Tue Jul 05 2005 - 14:36:43 CDT)
  • Re: AMBER: estimation of interface size (Mon Jul 04 2005 - 06:39:11 CDT)
  • Re: AMBER: MM-PBSA-big energies (Sun Jul 03 2005 - 17:13:48 CDT)
  • Re: AMBER: fail of minimization in sander (Thu Jun 16 2005 - 06:06:42 CDT)
  • Re: AMBER: fail of minimization in sander (Wed Jun 15 2005 - 06:24:04 CDT)
  • Re: AMBER: Extended bonds-MD (Wed Jun 15 2005 - 06:22:29 CDT)
  • Re: AMBER: transfer data from Linux to windows (Thu Jun 09 2005 - 17:41:26 CDT)
  • Re: AMBER: GB/SA/LD parallel sander (Wed Jun 08 2005 - 15:09:59 CDT)
  • Re: AMBER: total energy leaps (Wed Jun 08 2005 - 06:22:06 CDT)
  • Re: AMBER: nucgen problem (Tue Jun 07 2005 - 14:34:17 CDT)
  • Re: AMBER: Solvate question? (Mon Jun 06 2005 - 11:13:37 CDT)
  • Re: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 11:12:38 CDT)
  • Re: AMBER: Solvate question? (Mon Jun 06 2005 - 06:26:53 CDT)
  • Re: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 06:24:25 CDT)
  • Re: AMBER: How does Amber8 implemnet ntf=4? (Thu Jun 02 2005 - 10:53:36 CDT)
  • Re: AMBER: question whem using leap (Thu Jun 02 2005 - 06:45:53 CDT)
  • Re: AMBER: if setting ntf=4, will it cause someproblem? (Tue May 31 2005 - 10:12:30 CDT)
  • Re: AMBER: Error: vlimit exceeded for step (Tue May 24 2005 - 12:51:14 CDT)
  • Re: AMBER: conformational sampling of a peptide (Tue May 24 2005 - 08:11:53 CDT)
  • Re: AMBER: Unexpected stop of Sander run (Mon May 23 2005 - 08:57:00 CDT)
  • Re: AMBER: Unexpected stop of Sander run (Mon May 23 2005 - 06:15:34 CDT)
  • Re: AMBER: Unexpected stop of Sander run (Sun May 22 2005 - 15:22:11 CDT)
  • Re: AMBER: Error in minimization (Fri May 20 2005 - 07:57:37 CDT)
  • Re: AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? (Sat May 14 2005 - 12:52:56 CDT)
  • Re: AMBER: the restraint MD fail with amber8,but success with amber7 (Fri May 13 2005 - 05:50:10 CDT)
  • Re: AMBER: langevin, GB and simulated annealing - 5 (Tue May 10 2005 - 06:58:42 CDT)
  • Re: AMBER: langevin, GB and simulated annealing - 5 (Mon May 09 2005 - 14:58:57 CDT)
  • Re: AMBER: strange VDWAALS and EEL energies calculated by pbsa (Fri Apr 22 2005 - 11:05:42 CDT)
  • Re: AMBER: intramolecular nonbonded interactions in AMBER force field (Thu Apr 21 2005 - 07:50:46 CDT)
  • Re: AMBER: intramolecular nonbonded interactions in AMBER force field (Wed Apr 20 2005 - 17:28:08 CDT)
  • Re: AMBER: langevin, GB and simulated annealing? (Mon Apr 18 2005 - 10:36:19 CDT)
  • Re: AMBER: the restart of replica exchange method (REM) simulations in AMBER8 (Sat Apr 16 2005 - 07:42:37 CDT)
  • Re: AMBER: Formatting a restraint file (Thu Apr 14 2005 - 11:13:49 CDT)
  • Re: AMBER: Formatting a restraint file (Wed Apr 13 2005 - 16:18:54 CDT)
  • Re: AMBER: Protein with structural ions (Tue Apr 12 2005 - 11:09:48 CDT)
  • Re: AMBER: rst file problems (Tue Apr 12 2005 - 08:39:02 CDT)
  • Re: AMBER: rst file problems (Mon Apr 11 2005 - 08:22:41 CDT)
  • Re: AMBER: Two question about dielectric constant (Mon Apr 11 2005 - 08:18:07 CDT)
  • Re: AMBER: average structure-ptraj (Sat Apr 09 2005 - 10:02:02 CDT)
  • Re: AMBER: GB with Langevin dynamics problem 2 (Fri Apr 08 2005 - 14:03:14 CDT)
  • Re: AMBER: Disulfide bond (Fri Apr 08 2005 - 09:54:46 CDT)
  • Re: AMBER: RE: system comparison for amber (Thu Apr 07 2005 - 12:00:18 CDT)
  • Re: AMBER: GB with Langevin dynamics problem (Tue Apr 05 2005 - 11:17:24 CDT)
  • Re: AMBER: force constant Unit used in TMD (Mon Apr 04 2005 - 11:06:45 CDT)
  • Re: AMBER: Sander minimization & dynamic question (Mon Apr 04 2005 - 06:48:26 CDT)
  • Re: AMBER: What does this mean .. ? (Thu Mar 31 2005 - 13:33:25 CST)
  • Re: AMBER: OH- dynamics (Wed Mar 30 2005 - 17:37:26 CST)
  • Re: AMBER: OH- dynamics (Wed Mar 30 2005 - 16:32:09 CST)
  • Re: AMBER: OH- dynamics (Wed Mar 30 2005 - 13:14:07 CST)
  • Re: AMBER: align snapshots to a reference (Wed Mar 30 2005 - 10:28:13 CST)
  • Re: AMBER: align snapshots to a reference (Wed Mar 30 2005 - 10:08:01 CST)
  • Re: AMBER: align snapshots to a reference (Tue Mar 29 2005 - 16:15:29 CST)
  • Re: AMBER: TMD force constant (Tue Mar 22 2005 - 07:57:01 CST)
  • Re: AMBER: question about periodicity of torsion parameter (Fri Mar 18 2005 - 16:51:40 CST)
  • Re: AMBER: Problems with Iodine (Fri Mar 18 2005 - 15:22:47 CST)
  • Re: AMBER: layer (Fri Mar 18 2005 - 10:01:45 CST)
  • Re: AMBER: Replica Exchange crashing (Fri Mar 18 2005 - 07:11:13 CST)
  • Re: AMBER: Separating solvent and solute energy in the microcanonical mode (Thu Mar 17 2005 - 17:33:43 CST)
  • Re: AMBER: Separating solvent and solute energy in the microcanonical mode (Thu Mar 17 2005 - 17:05:17 CST)
  • Re: AMBER: in vacuo parameters (Tue Mar 15 2005 - 17:29:31 CST)
  • Re: AMBER: frcmod.mod_phipsi.2 (Tue Mar 15 2005 - 16:52:53 CST)
  • Re: AMBER: Hydrogen bonding question (Tue Mar 15 2005 - 09:48:41 CST)
  • Re: AMBER: Hydrogen bonding question (Tue Mar 15 2005 - 09:21:37 CST)
  • Re: Re :AMBER: Holes in water (Sat Mar 12 2005 - 12:46:24 CST)
  • Re: Re :AMBER: Holes in water (Sat Mar 12 2005 - 12:32:06 CST)
  • Re: AMBER: A problem about removing waters and counterions by ptraj (Mon Mar 07 2005 - 07:29:14 CST)
  • Re: AMBER: Sample more conformational space (Wed Mar 02 2005 - 10:35:18 CST)
  • Re: AMBER: mpirun sander8 problem (Wed Feb 23 2005 - 07:05:01 CST)
  • Re: AMBER: lastrst (Tue Feb 22 2005 - 19:39:37 CST)
  • Re: AMBER: minimizing structures before MM-PBSA? (Tue Feb 22 2005 - 19:37:18 CST)
  • Re: AMBER: Restraint of atoms during minimization (Tue Feb 22 2005 - 11:28:01 CST)
  • Re: AMBER: vlimit exceeded and temperature blow up (Tue Feb 22 2005 - 10:46:21 CST)
  • Re: AMBER: Restraint of atoms during minimization (Tue Feb 22 2005 - 10:34:06 CST)
  • Re: AMBER: restraint only for Z cartegian coordinate? (Tue Feb 22 2005 - 10:02:31 CST)
  • Re: AMBER: amber8 and moil-view (Fri Feb 18 2005 - 14:13:03 CST)
  • Re: AMBER: molecule blowing apart during equilibration (Fri Feb 18 2005 - 14:11:49 CST)
  • Re: AMBER: amber8 and moil-view (Thu Feb 17 2005 - 14:06:42 CST)
  • Re: AMBER: amber8 and moil-view (Thu Feb 17 2005 - 13:42:13 CST)
  • Re: AMBER: Moil view trajectory clusters (Thu Feb 17 2005 - 12:19:50 CST)
  • Re: AMBER: moil-view (Thu Feb 17 2005 - 10:28:15 CST)
  • Re: AMBER: rms (Wed Feb 16 2005 - 07:59:43 CST)
  • Re: AMBER: Cyclic peptide (Wed Feb 16 2005 - 07:00:29 CST)
  • Re: AMBER: (Wed Feb 16 2005 - 06:55:57 CST)
  • Re: AMBER: soft-cores and Amber (Tue Feb 15 2005 - 17:11:14 CST)
  • Re: AMBER: Topology Format Amber 8 (Tue Feb 15 2005 - 06:42:29 CST)
  • Re: AMBER: inconsistent ordering in an improper dihedral of TRP (Fri Feb 11 2005 - 17:41:26 CST)
  • Re: AMBER: too much vacuum in the box created by Leap (Fri Feb 11 2005 - 07:21:23 CST)
  • Re: AMBER: Can REM be used as multiple normal sander jobs on parallel machine (Wed Feb 09 2005 - 18:03:55 CST)
  • Re: AMBER: problem in minimization (Tue Feb 08 2005 - 15:47:30 CST)
  • Re: AMBER: How to calculate RESTRAINT value (Tue Feb 08 2005 - 07:01:46 CST)
  • Re: AMBER: Dynamics error (Tue Feb 08 2005 - 06:59:04 CST)
  • Re: AMBER: N Metyl amino acids (Tue Feb 01 2005 - 06:47:30 CST)
  • Re: AMBER: replica exchange trouble with unit 6 (Thu Jan 27 2005 - 09:10:20 CST)
  • Re: AMBER: sander failure (Thu Jan 20 2005 - 16:20:00 CST)
  • Re: AMBER: problem with position restraints (refc file) (Tue Jan 18 2005 - 11:36:55 CST)
  • Re: AMBER: problem with position restraints (refc file) (Tue Jan 18 2005 - 10:03:03 CST)
  • Re: AMBER: GB differences between AMBER7 and AMBER8 (Tue Jan 18 2005 - 08:08:20 CST)
  • Re: AMBER: Sander Replica Exchange exits with unit 6 error (Mon Jan 17 2005 - 11:17:56 CST)
  • Re: AMBER: Sander Replica Exchange exits with unit 6 error (Mon Jan 17 2005 - 08:45:56 CST)
  • Re: AMBER: Sander Replica Exchange exits with unit 6 error] (Mon Jan 17 2005 - 07:58:20 CST)
  • Re: AMBER: Coordinate Superimposition in PTRAJ (Sun Jan 16 2005 - 08:56:30 CST)
  • Re: AMBER: amber8 parallel sander (Wed Jan 12 2005 - 09:30:22 CST)
  • Re: AMBER: amber8 parallel sander (Wed Jan 12 2005 - 08:03:32 CST)
  • Re: AMBER: van der waals parameters (Wed Jan 12 2005 - 06:41:31 CST)
  • Re: AMBER: amber8 parallel sander (Wed Jan 12 2005 - 06:38:30 CST)
  • Re: AMBER: Steered Molecular Dynamics with AMBER? (Tue Jan 04 2005 - 16:47:38 CST)
  • Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied (Tue Jan 04 2005 - 06:47:03 CST)
• case
  • RE: AMBER: Amber 8: questions about free energy perturbation (Mon Sep 12 2005 - 02:29:15 CDT)
• cbala_at_igib.res.in
  • RE: AMBER: sander prob (Mon Sep 19 2005 - 10:57:58 CDT)
  • Re: AMBER: sander prob (Sat Sep 17 2005 - 05:28:51 CDT)
  • AMBER: sander prob (Fri Sep 16 2005 - 03:18:42 CDT)
  • Re: AMBER: amber8installation (Fri Aug 19 2005 - 10:33:44 CDT)
  • AMBER: amber8installation (Fri Aug 19 2005 - 07:53:03 CDT)
  • Re: AMBER: loading DNA-RNA hybrid in xleap (Sat Jul 02 2005 - 14:57:33 CDT)
  • AMBER: loading DNA-RNA hybrid in xleap (Sat Jul 02 2005 - 10:36:59 CDT)
  • Re: AMBER: nucgen problem (Tue Jun 07 2005 - 14:48:13 CDT)
  • AMBER: nucgen problem (Tue Jun 07 2005 - 08:41:27 CDT)
  • AMBER: error during MD run (Wed May 18 2005 - 13:39:25 CDT)
  • AMBER: loading pdb (Wed May 18 2005 - 00:56:13 CDT)
• Cenk Andac
  • AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU (Sat Dec 31 2005 - 12:24:30 CST)
  • CORRENDUM: Re: AMBER: mm_pbsa (Sat Nov 12 2005 - 02:31:27 CST)
  • Re: AMBER: mm_pbsa (Thu Nov 10 2005 - 08:08:24 CST)
  • Re: AMBER: mm_pbsa problem (Tue Nov 01 2005 - 02:15:23 CST)
  • AMBER: QMMM for copper complexes! (Mon Oct 24 2005 - 12:12:22 CDT)
  • AMBER: Is MM-PBSA doable for transition metals ? (Mon Oct 24 2005 - 11:55:27 CDT)
  • Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED (Mon Oct 24 2005 - 11:43:36 CDT)
  • Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED (Mon Oct 24 2005 - 11:12:30 CDT)
  • AMBER: Problem with the QMMM example in AMBER 2004 tutorial (Sun Oct 23 2005 - 11:31:45 CDT)
  • Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED (Sat Oct 22 2005 - 13:02:00 CDT)
  • Problem solved! Re: AMBER: How to get PDB structures optimized for RED-II (Sat Oct 22 2005 - 12:38:58 CDT)
  • Re: AMBER: How to get PDB structures optimized for RED-II (Fri Oct 14 2005 - 12:14:02 CDT)
  • Re: AMBER: How to get PDB structures optimized for RED-II (Sat Oct 08 2005 - 08:34:42 CDT)
  • AMBER: How to get PDB structures optimized for RED-II (Tue Sep 06 2005 - 03:49:13 CDT)
  • Re: AMBER: RED-II failure to recognize GAMESS output (Tue Sep 06 2005 - 03:30:19 CDT)
  • AMBER: RED-II failure to recognize GAMESS output (Fri Sep 02 2005 - 15:47:07 CDT)
  • AMBER: Reference (?) for normal-mode analysis in nmode (Mon May 30 2005 - 04:18:59 CDT)
  • Re:Re: AMBER: Solute-solvent boundary in pbsa (Thu May 26 2005 - 15:58:55 CDT)
  • AMBER: antechamber, reference? (Wed May 25 2005 - 16:14:48 CDT)
  • Re#2:Re: AMBER: Solute-solvent boundary in pbsa (Wed May 25 2005 - 15:03:47 CDT)
  • Re: AMBER: Solute-solvent boundary in pbsa (Wed May 25 2005 - 11:21:52 CDT)
  • Solute-solvent boundary in pbsa ..Re: AMBER: Copyright for PBSA (Tue May 24 2005 - 13:48:26 CDT)
  • AMBER: Copyright for PBSA (Sat May 21 2005 - 03:32:00 CDT)
  • AMBER: Citing the PBSA module of AMBER8 (Fri May 20 2005 - 16:27:03 CDT)
  • AMBER: MM_PBSA for NMR restrained structures (Fri May 20 2005 - 03:36:10 CDT)
  • Re: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue (Thu May 19 2005 - 12:03:43 CDT)
  • Re: AMBER: Meaning of induced dipole moments for atom pairs? (Thu May 05 2005 - 19:28:49 CDT)
  • AMBER: Meaning of induced dipole moments for atom pairs? (Wed May 04 2005 - 15:52:06 CDT)
  • AMBER: ipol=1 & use_pme= ?? (Sat Apr 30 2005 - 08:26:57 CDT)
  • Re: AMBER: Induced dipole in AMBER8 (Mon Apr 25 2005 - 14:00:17 CDT)
  • AMBER: Induced dipole in AMBER8 (Fri Apr 22 2005 - 11:57:56 CDT)
  • AMBER: antechamber and multiplicity (Mon Mar 14 2005 - 13:57:27 CST)
  • Re:Re: AMBER: Cu++ and RED (Sat Mar 12 2005 - 12:39:10 CST)
  • Re: AMBER: Cu++ and RED (Sat Mar 12 2005 - 06:28:34 CST)
  • AMBER: Citing Generalized Born Implicit solvent Model (igb=5) (Sun Mar 06 2005 - 18:57:21 CST)
  • AMBER: rotameric populations? (Thu Feb 17 2005 - 09:15:05 CST)
  • Re: AMBER: Cu++ and RED (Mon Feb 14 2005 - 23:30:47 CST)
  • RE: AMBER: running shell scripts in tleap? (Mon Feb 14 2005 - 23:24:44 CST)
  • AMBER: running shell scripts in tleap? (Mon Feb 14 2005 - 16:23:44 CST)
  • AMBER: Cu++ and RED (Fri Feb 11 2005 - 03:46:13 CST)
  • Re: AMBER: &dipoles in sander (Fri Jan 28 2005 - 13:25:36 CST)
  • RE: AMBER: problem with pressure equilibration (Fri Jan 28 2005 - 13:18:02 CST)
  • RE: AMBER: &dipoles in sander (Fri Jan 28 2005 - 04:04:21 CST)
  • AMBER: problem with pressure equilibration (Thu Jan 27 2005 - 16:23:59 CST)
  • RE: AMBER: &dipoles in sander (Sat Jan 22 2005 - 03:47:50 CST)
  • AMBER: &dipoles in sander (Fri Jan 21 2005 - 05:59:47 CST)
  • AMBER: Copper library? (Mon Jan 10 2005 - 12:31:51 CST)
  • RE: AMBER: Questions about sander.QMMM (Sat Jan 08 2005 - 03:57:22 CST)
  • AMBER: Questions about sander.QMMM (Fri Jan 07 2005 - 09:51:56 CST)
  • Re: AMBER: Problem with computing Resp charges using RED (Sat Jan 01 2005 - 08:08:24 CST)
• chai ann ng
  • Re: AMBER: Cyclohexane solvent Box (Mon Oct 17 2005 - 09:27:13 CDT)
• chaiann ng
  • RE: AMBER: Density of Cyclohexane box (Thu Nov 03 2005 - 21:10:50 CST)
  • AMBER: Density of Cyclohexane box (Wed Nov 02 2005 - 21:57:49 CST)
  • AMBER: Cyclohexane solvent Box (Sun Oct 16 2005 - 23:43:21 CDT)
  • AMBER: Opinion needed-Solvents (Wed Aug 31 2005 - 20:59:00 CDT)
  • AMBER: advice needed for minimization and dynamic protocol (Thu Jun 02 2005 - 20:33:44 CDT)
  • AMBER: charges difference of atom in xleap and prmtop (Tue May 24 2005 - 23:02:33 CDT)
  • RE: AMBER: how to generate frcmod file for using prepin file.. (Mon May 23 2005 - 22:03:55 CDT)
  • RE: AMBER: read pdb back to xleap after solvation of chloroform (Thu May 19 2005 - 21:55:23 CDT)
  • RE: AMBER: read pdb back to xleap after solvation of chloroform (Thu May 19 2005 - 21:05:27 CDT)
  • Re: AMBER: read pdb back to xleap after solvation of chloroform (Thu May 19 2005 - 20:59:47 CDT)
  • AMBER: read pdb back to xleap after solvation of chloroform (Thu May 19 2005 - 20:19:04 CDT)
  • AMBER: Sander minimization & dynamic question (Mon Apr 04 2005 - 05:45:48 CDT)
  • AMBER: solvateoct mymolecule CHCL3BOX 10 PROBLEM!!! (Thu Mar 31 2005 - 22:30:40 CST)
• Charles Karney
  • AMBER: Using Antechamber with Gamess and other molecular manipulations (Mon Jul 18 2005 - 12:28:20 CDT)
• Chen Chengwen
  • AMBER: Setting Amber force field parameters (Mon May 23 2005 - 02:55:38 CDT)
  • AMBER: platinum atom in Xleap (Fri May 13 2005 - 21:11:12 CDT)
• Chen Hu
  • AMBER: Problem when converting AMBER trajectories to CHARMM format (Sat Apr 23 2005 - 17:20:56 CDT)
• Chng Choon-Peng
  • Re: AMBER: PMEMD limitation on NFFT (Fri Nov 04 2005 - 21:44:58 CST)
  • AMBER: PMEMD limitation on NFFT (Fri Nov 04 2005 - 18:38:38 CST)
• Chris Harrison
  • Re: AMBER: Installation problem (Mon Jun 13 2005 - 19:33:13 CDT)
  • Re: AMBER: Installation problem (Sun Jun 12 2005 - 18:04:22 CDT)
• Chris Moth
  • AMBER: Tyrosine CZ Parameterization Bug continues in Amber 8 (Thu Sep 01 2005 - 17:04:21 CDT)
  • Re: AMBER: how is truncated octahedron box calculated (Thu Jul 07 2005 - 16:50:24 CDT)
  • AMBER: Dr. Cornell's calculation of Sulfur vdw epsilon value in parm94.dat? (Fri May 06 2005 - 14:32:23 CDT)
  • Re: AMBER: stereo (Wed Feb 09 2005 - 14:02:13 CST)
  • AMBER: Manuals need update: protonate -b and -c options gone in Amber 7 and 8 (Mon Jan 31 2005 - 15:39:56 CST)
  • AMBER: General Question about AMBER's Free Energy Perturbation Method (Wed Jan 05 2005 - 16:06:33 CST)
• Christoph Brockmann
  • AMBER: nmropt =1 AND ntr=1 in pmemd (Tue Jun 14 2005 - 04:33:39 CDT)
• Christophe Guilbert
  • AMBER: Antechamber/Leap, problem with Improper angles (Mon Nov 14 2005 - 20:06:28 CST)
• Chunhu Tan
  • Re: AMBER: Question about NVE simulation. (Tue Oct 18 2005 - 14:39:43 CDT)
  • AMBER: How to simulate a crystal structure? (Tue Oct 11 2005 - 18:22:39 CDT)
  • AMBER: How to build a crystal structure from a unit cell pdb? (Tue Sep 20 2005 - 13:55:06 CDT)
• Chutintorn Punwong
  • Re: AMBER: question about loadiing pdb file of a molecule complex (Fri May 27 2005 - 17:07:52 CDT)
• Claire Zerafa
  • Re: AMBER: PARM-99 (Sat Nov 26 2005 - 03:24:25 CST)
  • AMBER: error in safe (Mon Oct 24 2005 - 08:18:50 CDT)
  • AMBER: Fw: pca with ptraj (Wed Oct 19 2005 - 07:02:08 CDT)
  • AMBER: pca with ptraj (Mon Oct 17 2005 - 18:11:21 CDT)
  • AMBER: PCA (Tue Oct 11 2005 - 08:33:49 CDT)
  • Re: AMBER: STARTING WHERE I LEFT OFF (Sat Sep 03 2005 - 12:49:31 CDT)
  • AMBER: STARTING WHERE I LEFT OFF (Sat Sep 03 2005 - 12:13:59 CDT)
  • AMBER: problem with protein ligand complex (Sat Jul 16 2005 - 11:31:56 CDT)
• claudio
  • AMBER: Free energy extimate for the same structure but different conformers (Mon Feb 21 2005 - 14:56:10 CST)
• Claudio Morgado
  • AMBER: GAFF: H type on carbon bearing a cyano group (Tue Apr 19 2005 - 03:34:12 CDT)
  • AMBER: gaff atom types (Fri Apr 15 2005 - 12:11:18 CDT)
  • AMBER: sander.QMMM and fcap (Thu Mar 17 2005 - 07:56:34 CST)
• Cordova, Luis E.
  • AMBER: question about spline in sander -- array size of eed_cub (Thu Jun 30 2005 - 23:33:25 CDT)
  • AMBER: precision switch from 64 to 32 bit (double from single precision) (Thu Jun 09 2005 - 00:39:59 CDT)
  • RE: AMBER: meaningful tax for sander question (Tue May 31 2005 - 15:03:59 CDT)
  • AMBER: meaningful tax for sander question (Tue May 31 2005 - 14:19:30 CDT)
  • AMBER: why is snaupe.f is empty? (Thu May 26 2005 - 12:06:24 CDT)
  • AMBER: amber8 test error (Thu May 12 2005 - 22:26:00 CDT)
• cristian obiol
  • Re: AMBER: does the result of H bond is consistent with the ?Eele of MM_PBSA? (Fri Dec 23 2005 - 05:01:42 CST)
  • AMBER: total energy leaps (Wed Jun 08 2005 - 05:44:18 CDT)
  • RE:AMBER: density problem (Wed Jun 08 2005 - 03:56:23 CDT)
  • RE:AMBER: density problem (Thu Jun 02 2005 - 03:14:21 CDT)
  • AMBER: density problem (Tue May 31 2005 - 04:17:46 CDT)
• cui wei
  • Re: AMBER: a quistion about compile (Mon Dec 19 2005 - 19:03:46 CST)
  • Re: AMBER: a quistion about compile (Mon Dec 19 2005 - 19:00:20 CST)
  • AMBER: a quistion about compile (Mon Dec 19 2005 - 06:10:07 CST)
  • Re: AMBER: question about mmpbsa (Tue Dec 13 2005 - 19:09:29 CST)
  • AMBER: question about mmpbsa (Tue Dec 13 2005 - 01:33:08 CST)
• Daisuke Katagiri
  • Re: AMBER: About Gaussian Key Words (fwd) (Mon Apr 11 2005 - 19:03:36 CDT)
• Daniel Oehme
  • AMBER: Linear Interaction Energy (Tue Sep 20 2005 - 20:39:53 CDT)
• Daniel Wetzler
  • AMBER: Problem with installation AMBER8 on Solaris 8 using original SUN compilers (Thu Sep 15 2005 - 06:46:14 CDT)
  • Re: AMBER: Amber 7 Compiler Error (Wed Jul 20 2005 - 04:38:25 CDT)
  • Re: AMBER: Problem with building AMBER7 on SUSE Linux 9.2 (Tue Jul 12 2005 - 02:53:40 CDT)
  • AMBER: Problem with building AMBER7 on SUSE Linux 9.2 (Fri Jul 08 2005 - 06:18:09 CDT)
  • AMBER: Re: AMBER: Problems with parameter lib and prep püarameter files (Wed Jul 06 2005 - 05:40:53 CDT)
  • AMBER: Problems with parameter lib and prep püarameter files (Mon Jul 04 2005 - 04:14:56 CDT)
  • AMBER: Searching for NAD parameter files / Problems with parameter file creation (Thu Jun 23 2005 - 09:43:29 CDT)
• Daniela Kohen
  • AMBER: Tutorial #1 ptraj/sander problem (Thu May 12 2005 - 17:03:07 CDT)
• darden
  • Re: AMBER: ew_legal.h (Tue Nov 15 2005 - 07:44:26 CST)
  • Re: AMBER: Amber 8: questions about free energy perturbation (Tue Sep 13 2005 - 10:13:14 CDT)
  • Re: AMBER: EWALD and belly not strictly correct (Wed Feb 16 2005 - 11:08:31 CST)
• Dave S Walker
  • RE: AMBER: runtime error in sander? (Mon Jun 20 2005 - 13:02:16 CDT)
  • AMBER: runtime error in sander? (Tue May 31 2005 - 12:07:13 CDT)
• David A. Case
  • Re: AMBER: ambpdb TER problems (Fri Dec 30 2005 - 12:05:10 CST)
  • Re: AMBER: problem of calculate the charge (Fri Dec 30 2005 - 11:58:47 CST)
  • Re: AMBER: ambpdb TER problems (Tue Dec 27 2005 - 14:30:48 CST)
  • Re: AMBER: distance restraint simulation (Tue Dec 27 2005 - 14:31:03 CST)
  • Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN (Tue Dec 27 2005 - 13:18:06 CST)
  • Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN (Tue Dec 27 2005 - 10:17:49 CST)
  • Re: AMBER: ambpdb TER problems (Mon Dec 26 2005 - 20:08:26 CST)
  • Re: AMBER: building amino acid based surfactants? (Mon Dec 26 2005 - 19:53:19 CST)
  • Re: AMBER: ambpdb TER problems (Fri Dec 23 2005 - 19:53:50 CST)
  • Re: AMBER: (no subject) (Fri Dec 23 2005 - 19:43:28 CST)
  • Re: AMBER: Amber crashes at simulation in the NVT ensemble with the periodic box equiilbrated in the NPT ensemble. (Thu Dec 22 2005 - 13:56:36 CST)
  • Re: AMBER: No skew or curtosis when zero variance in moment (Thu Dec 22 2005 - 12:14:25 CST)
  • Re: AMBER: a quistion about compile (Wed Dec 21 2005 - 15:01:52 CST)
  • Re: AMBER: a quistion about compile (Tue Dec 20 2005 - 10:56:58 CST)
  • Re: AMBER: Atoms restrain (Mon Dec 19 2005 - 10:20:25 CST)
  • Re: AMBER: a quistion about compile (Mon Dec 19 2005 - 10:22:58 CST)
  • Re: AMBER: nmode error: GNORM is greater than the requested maximum (Fri Dec 16 2005 - 16:08:21 CST)
  • Re: AMBER: aniso and iso (Thu Dec 15 2005 - 10:28:28 CST)
  • Re: AMBER: How to add water to calculate MMPBSA (Wed Dec 14 2005 - 17:50:13 CST)
  • Re: AMBER: reading frcmod torsional parameters (Mon Dec 12 2005 - 10:56:02 CST)
  • Re: AMBER: Relax in tLEaP ? (Wed Dec 07 2005 - 13:58:43 CST)
  • Re: AMBER: hi (Wed Dec 07 2005 - 14:01:52 CST)
  • Re: AMBER: Alignment tensor and Interia tensor (Sat Dec 03 2005 - 13:05:30 CST)
  • AMBER: parmchk bug fix, with attachment (Fri Dec 02 2005 - 22:33:20 CST)
  • AMBER: parmchk bug fix (Fri Dec 02 2005 - 22:22:21 CST)
  • Re: AMBER: Using OPLS atom types (Fri Dec 02 2005 - 22:01:17 CST)
  • Re: AMBER: Creating an Ester with Antechamber/Gaff (Fri Dec 02 2005 - 22:05:16 CST)
  • Re: AMBER: rotational motion in periodic simulation (Fri Dec 02 2005 - 17:06:22 CST)
  • Re: AMBER: Mg2+ issues of using MM-PB/GBSA (Thu Dec 01 2005 - 13:47:20 CST)
  • Re: AMBER: MD without a thermostat (Thu Dec 01 2005 - 13:42:51 CST)
  • Re: AMBER: Residual Dipolar Refinement (Thu Dec 01 2005 - 08:22:11 CST)
  • AMBER: more data points on the parmchk problem (Wed Nov 30 2005 - 09:30:12 CST)
  • AMBER: parmchk segfaulting (Tue Nov 29 2005 - 22:06:03 CST)
  • Re: AMBER: AMBER compilation with -DREM (Tue Nov 29 2005 - 11:40:18 CST)
  • Re: AMBER: Cluster - input files (Mon Nov 28 2005 - 15:28:14 CST)
  • Re: AMBER: Cluster - input files (Mon Nov 28 2005 - 12:47:12 CST)
  • Re: AMBER: Comparing EELEC from amber and that calculated in the trivial fashion. (Mon Nov 28 2005 - 00:12:55 CST)
  • Re: AMBER: reordering atoms after antechamber (Fri Nov 25 2005 - 11:19:28 CST)
  • Re: AMBER: MM_PBSA question (Thu Nov 24 2005 - 12:25:56 CST)
  • Re: AMBER: gaff sugar residue instability (Thu Nov 24 2005 - 12:28:23 CST)
  • Re: AMBER: Leap handling crystallographic waters (Tue Nov 22 2005 - 14:08:39 CST)
  • Re: AMBER: RE: gaff sugar residue instability (Tue Nov 22 2005 - 13:40:18 CST)
  • Re: AMBER: MM_PBSA problem (Tue Nov 22 2005 - 10:49:59 CST)
  • Re: AMBER: sp0 console message after using addAtomTypes (Tue Nov 22 2005 - 10:44:30 CST)
  • Re: AMBER: ANAL problem (Mon Nov 21 2005 - 18:17:14 CST)
  • Re: AMBER: Will Amber 9 available? (Mon Nov 21 2005 - 10:28:34 CST)
  • Re: AMBER: Will Amber 9 available? (Sun Nov 20 2005 - 20:16:09 CST)
  • Re: AMBER: Question about PDB format (Sat Nov 19 2005 - 12:47:45 CST)
  • Re: AMBER: MM/PBSA basic questions (Fri Nov 18 2005 - 11:09:05 CST)
  • Re: AMBER: Polarization & energy analysis (Fri Nov 18 2005 - 11:05:43 CST)
  • Re: AMBER: using periodic boundary conditions to create infinite double helix (Wed Nov 16 2005 - 18:10:17 CST)
  • Re: AMBER: Resp install problem, again (Wed Nov 16 2005 - 15:53:27 CST)
  • Re: AMBER: Resp install problem, again (Wed Nov 16 2005 - 12:43:13 CST)
  • Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list (Wed Nov 16 2005 - 10:56:44 CST)
  • Re: AMBER: Antechamber/Leap, problem with Improper angles (Tue Nov 15 2005 - 15:03:11 CST)
  • Re: AMBER: calculating end-end distance (Tue Nov 15 2005 - 10:24:01 CST)
  • Re: AMBER: ew_legal.h (Mon Nov 14 2005 - 23:41:54 CST)
  • Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list (Mon Nov 14 2005 - 11:01:25 CST)
  • Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list (Fri Nov 11 2005 - 20:58:21 CST)
  • Re: AMBER: Resp install problem, again (Thu Nov 10 2005 - 11:39:49 CST)
  • Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list (Thu Nov 10 2005 - 11:00:12 CST)
  • Re: AMBER: Resp install problem (Wed Nov 09 2005 - 17:51:10 CST)
  • Re: AMBER: Time Correlation Functions with Amber (Tue Nov 08 2005 - 12:43:55 CST)
  • Re: AMBER: tkbc2 (Tue Nov 08 2005 - 10:50:51 CST)
  • Re: AMBER: Time Correlation Functions with Amber (Tue Nov 08 2005 - 10:25:50 CST)
  • Re: AMBER: bug report (Mon Nov 07 2005 - 10:36:29 CST)
  • Re: AMBER: tRNA's modified bases in the Amber parameters database (Mon Nov 07 2005 - 10:26:41 CST)
  • Re: AMBER: Improper Torsional Parameters (Thu Nov 03 2005 - 18:41:53 CST)
  • Re: AMBER: Antechamber error (Thu Nov 03 2005 - 17:06:35 CST)
  • Re: AMBER: fedora installation problem (Thu Nov 03 2005 - 12:50:42 CST)
  • Re: AMBER: REM difficulties (Thu Nov 03 2005 - 12:41:40 CST)
  • Re: AMBER: Leap error: Could not find atom type: CE (Wed Nov 02 2005 - 12:57:59 CST)
  • Re: AMBER: rounding in xleap when using saveoff command... (Wed Nov 02 2005 - 10:50:41 CST)
  • Re: AMBER: Improper Torsional Parameters (Wed Nov 02 2005 - 10:47:34 CST)
  • Re: AMBER: Unknown atomtypes in amber (Sat Oct 29 2005 - 12:06:20 CDT)
  • Re: AMBER: problems installing amber 7 on a RH Linux 8 machine (Thu Oct 27 2005 - 14:33:33 CDT)
  • Re: AMBER: parmchk error : Cannot open CONNECT.TPL, exit (Tue Oct 25 2005 - 16:16:35 CDT)
  • Re: AMBER: xleap with modified residue (Mon Oct 24 2005 - 12:36:40 CDT)
  • Re: AMBER: rdparm: a parameter array overflowed (Mon Oct 24 2005 - 11:00:50 CDT)
  • Re: Re: AMBER: delphi and surface in MMPBSA (Sat Oct 22 2005 - 11:44:37 CDT)
  • Re: AMBER: Dipolar coupling refinement (Fri Oct 21 2005 - 20:03:43 CDT)
  • Re: AMBER: antechamber -- missing improper torsions (Fri Oct 21 2005 - 12:57:31 CDT)
  • Re: (2) Re: AMBER: F,Cl,Br,I in MMPBSA (Fri Oct 21 2005 - 10:31:06 CDT)
  • Re: AMBER: amber file formats. (Thu Oct 20 2005 - 16:32:29 CDT)
  • Re: AMBER: amber file formats. (Thu Oct 20 2005 - 11:20:36 CDT)
  • Re: AMBER: delphi and surface in MMPBSA (Thu Oct 20 2005 - 11:06:15 CDT)
  • Re: AMBER: GNU Autotool integration for Amber8! (Wed Oct 19 2005 - 18:41:32 CDT)
  • Re: AMBER: GNU Autotool integration for Amber8! (Tue Oct 18 2005 - 11:54:37 CDT)
  • Re: AMBER: sander error (Tue Oct 18 2005 - 09:59:39 CDT)
  • Re: AMBER: F,Cl,Br,I in MMPBSA (Mon Oct 17 2005 - 10:10:17 CDT)
  • Re: AMBER: AMBER goes in a Loop (Fri Oct 14 2005 - 10:05:41 CDT)
  • Re: AMBER: Scaling factor of NMR restraint (Fri Oct 14 2005 - 10:00:01 CDT)
  • Re: AMBER: How to simulate a crystal structure? (Wed Oct 12 2005 - 10:17:35 CDT)
  • Re: AMBER: warning in leap (Tue Oct 11 2005 - 17:17:20 CDT)
  • Re: AMBER: PCA (Tue Oct 11 2005 - 09:32:36 CDT)
  • Re: AMBER: sander error (Tue Oct 11 2005 - 09:27:20 CDT)
  • Re: AMBER: Minimization in sander and nmode (Thu Oct 06 2005 - 05:06:33 CDT)
  • Re: AMBER: Problem finding transition state using NMODE (Thu Sep 22 2005 - 09:56:59 CDT)
  • Re: AMBER: D-enantiomers (Tue Sep 20 2005 - 18:07:53 CDT)
  • Re: AMBER: GB refinement of CYANA structures (Fri Sep 16 2005 - 16:40:37 CDT)
  • Re: AMBER: Amber 8: questions about free energy perturbation (Fri Sep 16 2005 - 04:00:13 CDT)
  • Re: AMBER: parralel test (Fri Sep 09 2005 - 14:07:16 CDT)
  • Re: AMBER: Error in MD run! (Fri Sep 02 2005 - 11:27:33 CDT)
  • Re: AMBER: Temperature regulation (Tue Aug 30 2005 - 17:45:13 CDT)
  • Re: AMBER: nmode minimization and normal mode calculation (Tue Aug 30 2005 - 09:38:14 CDT)
  • Re: AMBER: mm_pbsa energy decomposition error (Wed Aug 24 2005 - 08:26:49 CDT)
  • Re: AMBER: difference of energy in sander and nmode in amber 7 (Thu Aug 18 2005 - 09:39:55 CDT)
  • Re: AMBER: difference of energy in sander and nmode in amber 7 (Wed Aug 17 2005 - 11:36:11 CDT)
  • Re: AMBER: leap question (Sat Aug 06 2005 - 06:33:44 CDT)
  • Re: AMBER: Convert .prmtop (AMBER7/8) to old format (AMBER6) (Sat Aug 06 2005 - 06:26:14 CDT)
  • Re: AMBER: leap question (Fri Aug 05 2005 - 17:34:39 CDT)
  • Re: AMBER: Error with antechamber (Fri Aug 05 2005 - 07:26:36 CDT)
  • Re: AMBER: coordinated water molecules deleted when addions (Mon Aug 01 2005 - 08:39:39 CDT)
  • Re: AMBER: Amber parameters for ADP (Sat Jul 30 2005 - 12:08:08 CDT)
  • Re: AMBER: Failed sander runs for large systems (Sat Jul 30 2005 - 11:57:14 CDT)
  • Re: AMBER: RESTARTED DUE TO LINMIN FAILURE (Sat Jul 30 2005 - 11:59:19 CDT)
  • Re: AMBER: ambpdb core dump (Fri Jul 29 2005 - 09:56:42 CDT)
  • Re: AMBER: ambpdb core dump (Fri Jul 29 2005 - 09:40:03 CDT)
  • Re: AMBER: Fatal Error on loading a pdb in xLeap (Thu Jul 28 2005 - 17:17:14 CDT)
  • Re: AMBER: cutoff in ANAL (Thu Jul 28 2005 - 11:26:40 CDT)
  • Re: AMBER: Adding residues to a DNA sequence (Wed Jul 27 2005 - 16:31:16 CDT)
  • Re: AMBER: new residue (Wed Jul 27 2005 - 16:13:32 CDT)
  • Re: AMBER: An atom name with 4 characters is not compatible with Leap ? (Wed Jul 27 2005 - 12:39:08 CDT)
  • Re: AMBER: new residue (Wed Jul 27 2005 - 12:20:42 CDT)
  • Re: AMBER: An atom name with 4 characters is not compatible with Leap ? (Wed Jul 27 2005 - 10:08:11 CDT)
  • Re: AMBER: prepi format and question about it (Wed Jul 27 2005 - 09:57:30 CDT)
  • Re: AMBER: Thermodynamic Integration for conformational changes? (Tue Jul 26 2005 - 13:42:54 CDT)
  • Re: AMBER: nucgen H5T H3T (Tue Jul 26 2005 - 09:54:32 CDT)
  • Re: AMBER: SHAKE error (Mon Jul 25 2005 - 18:57:02 CDT)
  • Re: AMBER: NTWPRY problem (Mon Jul 25 2005 - 18:54:25 CDT)
  • Re: AMBER: antechamber (Mon Jul 25 2005 - 18:42:32 CDT)
  • Re: AMBER: Adding residues to a DNA sequence (Mon Jul 25 2005 - 16:39:23 CDT)
  • Re: AMBER: [OT] A nab programming question (Mon Jul 25 2005 - 16:35:49 CDT)
  • Re: AMBER: nucgen bdna types (Sun Jul 24 2005 - 18:42:44 CDT)
  • Re: AMBER: SHAKE error (Fri Jul 22 2005 - 15:46:42 CDT)
  • Re: AMBER: Question about Prep file (Fri Jul 22 2005 - 13:34:57 CDT)
  • Re: AMBER: An atom name with 4 characters is not compatible with Leap ? (Fri Jul 22 2005 - 12:24:58 CDT)
  • Re: AMBER: An atom name with 4 characters is not compatible with Leap ? (Fri Jul 22 2005 - 12:27:31 CDT)
  • Re: AMBER: SHAKE error (Fri Jul 22 2005 - 11:04:15 CDT)
  • Re: AMBER: problem with xleap (Fri Jul 22 2005 - 10:59:24 CDT)
  • Re: AMBER: FW: (Tue Jul 19 2005 - 21:46:48 CDT)
  • Re: AMBER: PMF calculations with TI using the sander (Mon Jul 18 2005 - 11:03:47 CDT)
  • Re: AMBER: cap simulations questions (Mon Jul 18 2005 - 11:01:34 CDT)
  • Re: AMBER: problem with protein ligand complex (Sat Jul 16 2005 - 14:05:02 CDT)
  • Re: AMBER: lib file for nonstandard residue (Thu Jul 14 2005 - 17:35:47 CDT)
  • Re: AMBER: Modeling of a radical (Thu Jul 14 2005 - 10:48:54 CDT)
  • Re: AMBER: Leap question (Thu Jul 14 2005 - 10:39:59 CDT)
  • Re: AMBER: MD simulation on a protein solvated by a combination of some water mod (Thu Jul 14 2005 - 10:29:20 CDT)
  • Re: AMBER: TI - frcmod file (Wed Jul 13 2005 - 16:10:56 CDT)
  • Re: AMBER: molsurf error in MM/PBSA calculation (Tue Jul 12 2005 - 20:23:50 CDT)
  • Re: AMBER: molsurf error in MM/PBSA calculation (Tue Jul 12 2005 - 17:03:23 CDT)
  • Re: AMBER: Anal - problems with energy analysis (Tue Jul 12 2005 - 17:00:45 CDT)
  • Re: AMBER: MM_PBSA help, please (Tue Jul 12 2005 - 11:34:56 CDT)
  • Re: AMBER: Question about "nmanal" (Tue Jul 12 2005 - 11:29:46 CDT)
  • Re: AMBER: Question about "nmanal" (Mon Jul 11 2005 - 11:15:32 CDT)
  • Re: AMBER: Leap compilation issues (Mon Jul 11 2005 - 00:13:04 CDT)
  • Re: AMBER: building nucleic acids (Sun Jul 10 2005 - 23:51:46 CDT)
  • Re: AMBER: infinite DNA (Fri Jul 08 2005 - 19:26:04 CDT)
  • Re: AMBER: Water simulation (Fri Jul 08 2005 - 19:13:37 CDT)
  • Re: AMBER: problem with addIons (Wed Jul 06 2005 - 17:41:21 CDT)
  • Re: AMBER: sander problem (Wed Jul 06 2005 - 17:30:59 CDT)
  • Re: AMBER: box size in explicit water (Wed Jul 06 2005 - 12:30:59 CDT)
  • Re: AMBER: AMBER on Mac OS X (Wed Jul 06 2005 - 10:36:08 CDT)
  • Re: AMBER: 10-12 potential and create atom type (Tue Jul 05 2005 - 17:03:09 CDT)
  • Re: AMBER: pmemd - bug report (Tue Jul 05 2005 - 12:38:09 CDT)
  • Re: AMBER: pmemd - bug report (Tue Jul 05 2005 - 12:43:18 CDT)
  • Re: AMBER: molecular dynamics simulation of protein containing Mg2+ cation (Sun Jul 03 2005 - 18:34:14 CDT)
  • Re: AMBER: loading DNA-RNA hybrid in xleap (Sat Jul 02 2005 - 12:30:58 CDT)
  • Re: AMBER: questions about topology file (Fri Jul 01 2005 - 15:24:02 CDT)
  • Re: AMBER: least square fit of snapshots in md trajectory to a reference frame (Fri Jul 01 2005 - 10:51:21 CDT)
  • Re: AMBER: Create new Unit (Thu Jun 30 2005 - 20:38:42 CDT)
  • Re: AMBER: antechamber error (Thu Jun 30 2005 - 16:38:11 CDT)
  • Re: AMBER: Re: TI tutorial (Wed Jun 29 2005 - 12:01:23 CDT)
  • Re: AMBER: Re: TI tutorial (Wed Jun 29 2005 - 09:30:31 CDT)
  • Re: AMBER: Re: TI tutorial (Tue Jun 28 2005 - 20:09:44 CDT)
  • Re: AMBER: Re: TI tutorial (Tue Jun 28 2005 - 10:49:53 CDT)
  • Re: AMBER: pb_pgb test fail (Mon Jun 27 2005 - 13:48:32 CDT)
  • Re: AMBER: a question about varying positions of dihedral restraints with step number (Fri Jun 24 2005 - 10:09:21 CDT)
  • Re: AMBER: large std error in entropy estimation (Thu Jun 23 2005 - 13:25:03 CDT)
  • Re: AMBER: fail of minimization in sander (Thu Jun 16 2005 - 09:44:21 CDT)
  • Re: AMBER: How to modify force constants and equalibrium values for standard residues (Thu Jun 16 2005 - 09:41:18 CDT)
  • Re: AMBER: Question about "quasih" (Wed Jun 15 2005 - 16:01:33 CDT)
  • Re: AMBER: Question about "quasih" (Wed Jun 15 2005 - 12:43:47 CDT)
  • Re: AMBER: atom type question (Wed Jun 15 2005 - 10:18:18 CDT)
  • Re: AMBER: bad atom type: H (Wed Jun 15 2005 - 10:09:17 CDT)
  • Re: AMBER: why the dipeptide always moving out the virtual box (Tue Jun 14 2005 - 17:50:03 CDT)
  • Re: AMBER: compiler (Tue Jun 14 2005 - 13:40:16 CDT)
  • Re: AMBER: Restrained-MD (Mon Jun 13 2005 - 18:10:00 CDT)
  • Re: AMBER: why the dipeptide always moving out the virtual box (Mon Jun 13 2005 - 17:55:19 CDT)
  • Re: AMBER: GBSA and thermodynamic ensemble (Mon Jun 13 2005 - 15:13:14 CDT)
  • Re: AMBER: atom type question (Mon Jun 13 2005 - 15:05:44 CDT)
  • Re: AMBER: Can constant pH be used for minimization? (Sat Jun 11 2005 - 07:42:51 CDT)
  • Re: AMBER: Make Distance restraints for non-standard residues (Fri Jun 10 2005 - 14:59:13 CDT)
  • Re: AMBER: TI tutorial in Amber 8 (Wed Jun 08 2005 - 23:27:42 CDT)
  • Re: AMBER: nmode with ibelly (Wed Jun 08 2005 - 23:30:01 CDT)
  • Re: AMBER: TI calculation using sander (Tue Jun 07 2005 - 20:32:34 CDT)
  • Re: AMBER: nucgen problem (Tue Jun 07 2005 - 15:17:12 CDT)
  • Re: AMBER: quadrupole in resp (Tue Jun 07 2005 - 12:30:12 CDT)
  • Re: AMBER: nmode with ibelly (Tue Jun 07 2005 - 09:41:41 CDT)
  • Re: AMBER: nucgen problem (Tue Jun 07 2005 - 09:38:15 CDT)
  • Re: AMBER: Protein dynamics. (Mon Jun 06 2005 - 17:37:10 CDT)
  • Re: AMBER: nmode with ibelly (Mon Jun 06 2005 - 15:09:08 CDT)
  • Re: AMBER: pressure output (Fri Jun 03 2005 - 10:05:59 CDT)
  • Re: AMBER: TI in Amber8 (Fri Jun 03 2005 - 10:04:45 CDT)
  • Re: AMBER: New problem of parallel sander (Fri Jun 03 2005 - 10:00:30 CDT)
  • Re: AMBER: How does Amber8 implemnet ntf=4? (Thu Jun 02 2005 - 10:52:10 CDT)
  • Re: AMBER: Protein ions? (Thu Jun 02 2005 - 10:25:07 CDT)
  • Re: AMBER: amber8 installation problems (Thu Jun 02 2005 - 10:07:19 CDT)
  • Re: AMBER: amber question about leap (Thu Jun 02 2005 - 10:05:12 CDT)
  • Re: AMBER: gaff.dat typo (Thu Jun 02 2005 - 10:01:58 CDT)
  • Re: AMBER: meaningful tax for sander question (Tue May 31 2005 - 14:59:20 CDT)
  • Re: AMBER: question about loadiing pdb file of a molecule complex (Tue May 31 2005 - 13:00:59 CDT)
  • Re: AMBER: Error on restrained MD equilibration (AMBER 7) (Tue May 31 2005 - 10:45:01 CDT)
  • Re: AMBER: Reference (?) for normal-mode analysis in nmode (Tue May 31 2005 - 10:30:10 CDT)
  • Re: AMBER: Force field modification problem (Tue May 31 2005 - 00:17:06 CDT)
  • Re: AMBER: Force field modification problem (Mon May 30 2005 - 11:21:00 CDT)
  • Re: AMBER: Antechamber RESP failed for large organic molecule (Mon May 30 2005 - 11:09:27 CDT)
  • Re: AMBER: question about loadiing pdb file of a molecule complex (Sun May 29 2005 - 00:29:53 CDT)
  • Re: AMBER: Mol2 to prepin file conversion (Thu May 26 2005 - 19:44:36 CDT)
  • Re: AMBER: dissolving micelle structure in water.. amber7 (Thu May 26 2005 - 11:30:17 CDT)
  • Re: AMBER: antechamber, reference? (Wed May 25 2005 - 16:36:19 CDT)
  • Re: AMBER: error in chirality.c? (Wed May 25 2005 - 10:21:48 CDT)
  • Re: AMBER: Which forcefield? (Wed May 25 2005 - 00:32:09 CDT)
  • Re: AMBER: charges difference of atom in xleap and prmtop (Wed May 25 2005 - 00:27:51 CDT)
  • Re: AMBER: Connecting two molecules (Mon May 23 2005 - 10:23:51 CDT)
  • Re: AMBER: Unexpected stop of Sander run (Mon May 23 2005 - 10:00:46 CDT)
  • Re: AMBER: Copyright for PBSA (Sat May 21 2005 - 22:37:45 CDT)
  • Re: AMBER: leap problem: savepdb (Fri May 20 2005 - 10:21:13 CDT)
  • Re: AMBER: Representation of cations in MD (Fri May 20 2005 - 10:16:15 CDT)
  • Re: AMBER: read pdb back to xleap after solvation of chloroform (Thu May 19 2005 - 20:38:49 CDT)
  • Re: AMBER: GB - igb=1 versus dielc=? (Thu May 19 2005 - 11:09:47 CDT)
  • Re: AMBER: Using amber4 generated prep files in amber8? (Thu May 19 2005 - 10:31:54 CDT)
  • Re: AMBER: Message in .out file (Wed May 18 2005 - 01:38:40 CDT)
  • Re: AMBER: gaff: ca-ca-c -o torsion parameter (Wed May 18 2005 - 01:38:33 CDT)
  • Re: AMBER: error with ptraj (Wed May 18 2005 - 01:38:22 CDT)
  • Re: AMBER: loading pdb (Wed May 18 2005 - 01:38:27 CDT)
  • Re: AMBER: output of force field info (Mon May 16 2005 - 19:16:55 CDT)
  • Re: AMBER: How to set constraint (Mon May 16 2005 - 10:42:27 CDT)
  • Re: AMBER: amber8 test error (Fri May 13 2005 - 12:11:27 CDT)
  • Re: AMBER: creating residues - charge assign problems (Fri May 13 2005 - 11:43:41 CDT)
  • Re: AMBER: a nomenclature question (Thu May 12 2005 - 17:18:20 CDT)
  • Re: AMBER: SANDER BOMB: volume of ucell too big (Thu May 12 2005 - 15:27:50 CDT)
  • Re: AMBER: Trouble with example tutorial (Thu May 12 2005 - 12:04:51 CDT)
  • Re: AMBER: AMBER8 Build on Linux x64 running Opterons (Thu May 12 2005 - 11:58:19 CDT)
  • Re: Fwd: Re: AMBER: AMBER Test (Thu May 12 2005 - 10:33:15 CDT)
  • Re: AMBER: Parameter for alpha-lactose (Thu May 12 2005 - 10:29:08 CDT)
  • Re: AMBER: langevin, GB and simulated annealing - 5 (Mon May 09 2005 - 18:18:04 CDT)
  • Re: AMBER: ibelly in nmode (Sat May 07 2005 - 11:44:21 CDT)
  • Re: AMBER: No vdW parameters for HO.. (Fri May 06 2005 - 09:38:16 CDT)
  • Re: AMBER: How can I read parm99.dat file? (Thu May 05 2005 - 10:10:59 CDT)
  • Re: AMBER: Meaning of induced dipole moments for atom pairs? (Wed May 04 2005 - 17:13:14 CDT)
  • Re: AMBER: How to fix the atom in NPT case? (Tue May 03 2005 - 19:16:33 CDT)
  • Re: AMBER: rborn(i) in egb.f (Tue May 03 2005 - 17:59:23 CDT)
  • Re: AMBER: NOE constraints (Tue May 03 2005 - 15:25:44 CDT)
  • Re: AMBER: rborn(i) in egb.f (Tue May 03 2005 - 15:23:14 CDT)
  • Re: AMBER: How to fix the atom in NPT case? (Mon May 02 2005 - 13:31:26 CDT)
  • Re: AMBER: ipol=1 & use_pme= ?? (Mon May 02 2005 - 11:44:47 CDT)
  • Re: AMBER: Induced dipole in AMBER8 (Fri Apr 22 2005 - 20:23:41 CDT)
  • Re: AMBER: Amber Installation (Fri Apr 22 2005 - 14:14:01 CDT)
  • Re: AMBER: strange VDWAALS and EEL energies calculated by pbsa (Fri Apr 22 2005 - 11:12:15 CDT)
  • Re: AMBER: intramolecular nonbonded interactions in AMBER force field (Thu Apr 21 2005 - 10:42:10 CDT)
  • Re: AMBER: Nose-Hoover thermostat (Thu Apr 21 2005 - 10:44:13 CDT)
  • Re: AMBER: ibelly not working (Thu Apr 21 2005 - 10:36:40 CDT)
  • Re: AMBER: On the role of neutralizing ions in GB-MD and GBSA (Thu Apr 21 2005 - 10:22:37 CDT)
  • Re: AMBER: GB and mm_pbsa.pl (Wed Apr 20 2005 - 12:18:35 CDT)
  • Re: AMBER: GB and mm_pbsa.pl (Wed Apr 20 2005 - 10:12:56 CDT)
  • Re: AMBER: langevin, GB and simulated annealing - 2 (Tue Apr 19 2005 - 19:04:56 CDT)
  • Re: AMBER: Non-Bonded Cutoff vs PME (Tue Apr 19 2005 - 16:35:51 CDT)
  • Re: AMBER: The effect appling paches (Tue Apr 19 2005 - 10:01:58 CDT)
  • AMBER: Amber compilation problem (Tue Apr 19 2005 - 09:59:27 CDT)
  • Re: AMBER: Gibbs compilation problem (Tue Apr 19 2005 - 09:50:12 CDT)
  • Re: AMBER: solvent accessible surface area (Tue Apr 19 2005 - 09:43:24 CDT)
  • Re: AMBER: Amber8 installation on IBM (power4) with SUSE 9.1 Linux (IBM XLF compiler) (Tue Apr 19 2005 - 09:40:30 CDT)
  • Re: AMBER: Re: Re: AMBER: ATTN REVISION (Mon Apr 18 2005 - 23:37:13 CDT)
  • Re: AMBER: ATTN REVISION (Mon Apr 18 2005 - 09:57:58 CDT)
  • Re: AMBER: dielectric constant (Mon Apr 18 2005 - 10:00:41 CDT)
  • Re: AMBER: amber8/antechamber installation problem (Sun Apr 17 2005 - 16:38:51 CDT)
  • Re: AMBER: parameters in gaff.dat (Fri Apr 15 2005 - 15:31:56 CDT)
  • Re: AMBER: how to make the prepin file for dimer and clusters of organic molecule in Amber7 (Fri Apr 15 2005 - 10:25:56 CDT)
  • Re: AMBER: parameters in gaff.dat (Fri Apr 15 2005 - 01:02:48 CDT)
  • Re: AMBER: About NAB (Thu Apr 14 2005 - 20:33:26 CDT)
  • Re: AMBER: big fluctuation in MM-PBSA/GA (Thu Apr 14 2005 - 18:33:00 CDT)
  • Re: AMBER: solvate water box (Thu Apr 14 2005 - 11:30:11 CDT)
  • Re: AMBER: Formatting a restraint file (Thu Apr 14 2005 - 11:28:23 CDT)
  • Re: AMBER: Antechamber -reorders atom sequence (Thu Apr 14 2005 - 09:53:17 CDT)
  • Re: AMBER: Watson-Crick restraints (Thu Apr 14 2005 - 00:37:16 CDT)
  • Re: AMBER: About NAB (Thu Apr 14 2005 - 00:10:51 CDT)
  • Re: AMBER: MM_PBSA problem (Wed Apr 13 2005 - 10:23:17 CDT)
  • Re: AMBER: a bimolecular reaction (Tue Apr 12 2005 - 11:59:07 CDT)
  • Re: AMBER: GB with Langevin dynamics - solution (Tue Apr 12 2005 - 11:56:34 CDT)
  • Re: AMBER: nscm (Tue Apr 12 2005 - 10:55:58 CDT)
  • Re: AMBER: problems with "protonate" (Mon Apr 11 2005 - 20:45:47 CDT)
  • Re: AMBER:FAD can't be minimized. (Mon Apr 11 2005 - 09:58:45 CDT)
  • Re: AMBER: Protein with structural ions (Mon Apr 11 2005 - 09:50:28 CDT)
  • Re: AMBER: Protein with structural ions (Sun Apr 10 2005 - 23:04:52 CDT)
  • Re: AMBER: leap single precision (Sun Apr 10 2005 - 00:27:52 CDT)
  • Re: AMBER: GB with Langevin dynamics problem 2 (Sun Apr 10 2005 - 00:34:48 CDT)
  • Re: AMBER: how to get the parameters for modified amino acid residue? (Sun Apr 10 2005 - 00:29:09 CDT)
  • Re: AMBER: GB with Langevin dynamics problem 2 (Fri Apr 08 2005 - 12:48:27 CDT)
  • Re: AMBER: Protein with structural ions (Fri Apr 08 2005 - 12:29:44 CDT)
  • AMBER: Announcment: Nucleic Acid Builder (NAB) version 5 is released (Fri Apr 08 2005 - 11:52:54 CDT)
  • Re: AMBER: problems with "protonate" (Fri Apr 08 2005 - 10:49:29 CDT)
  • Re: AMBER: Protein with structural ions (Fri Apr 08 2005 - 10:41:22 CDT)
  • Re: AMBER: makeDIST_RST ERROR (Fri Apr 08 2005 - 10:36:30 CDT)
  • Re: AMBER: value of SALTCON (Thu Apr 07 2005 - 13:25:50 CDT)
  • Re: AMBER: FW: Amber installation (Wed Apr 06 2005 - 16:39:42 CDT)
  • Re: AMBER: Problems with protonate on Linux (Wed Apr 06 2005 - 11:19:11 CDT)
  • Re: AMBER: AMBER 8.0 problems with impose (tleap) on linux (Tue Apr 05 2005 - 23:48:14 CDT)
  • Re: AMBER: doble C and N terminal (Tue Apr 05 2005 - 16:25:10 CDT)
  • Re: AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters (Tue Apr 05 2005 - 10:31:15 CDT)
  • Re: AMBER: single-stranded poly(rC) simulation (Tue Apr 05 2005 - 01:31:35 CDT)
  • Re: AMBER: ff02EP + pol3 (2) (Tue Apr 05 2005 - 01:28:22 CDT)
  • Re: AMBER: (Tue Apr 05 2005 - 01:06:34 CDT)
  • Re: AMBER: problem with input files when using ff02EP + pol3 (Mon Apr 04 2005 - 00:18:29 CDT)
  • Re: AMBER: Problems with protonate on Linux (Fri Apr 01 2005 - 11:34:17 CST)
  • Re: AMBER: How to fix the torsion angles during energy minimization (Fri Apr 01 2005 - 11:24:37 CST)
  • Re: AMBER: scaleCharges with polarisable force fields (Fri Apr 01 2005 - 10:31:22 CST)
  • Re: AMBER: GB dynamics (Fri Apr 01 2005 - 10:16:46 CST)
  • Re: AMBER: how to cap regions (Thu Mar 31 2005 - 09:45:26 CST)
  • Re: AMBER: All the tests passed except prmtop and prepin... (Thu Mar 31 2005 - 09:40:18 CST)
  • Re: AMBER: "The system has extended beyond" error (Wed Mar 30 2005 - 09:08:07 CST)
  • Re: AMBER: tleap,xleap bond order for triple bonds (Tue Mar 29 2005 - 22:43:39 CST)
  • Re: AMBER: Are the constant pH simulations with explicit water possible? (Tue Mar 29 2005 - 11:37:27 CST)
  • Re: AMBER: vlimit exceeded in thermalization (Tue Mar 29 2005 - 11:22:20 CST)
  • Re: AMBER: antechamber availability (Thu Mar 24 2005 - 12:42:49 CST)
  • Re: AMBER: nonbonded interaction (Tue Mar 22 2005 - 23:38:08 CST)
  • Re: AMBER: substrate exit from protein in Amber 8.0 TI vdw simulation (Mon Mar 21 2005 - 12:27:40 CST)
  • Re: AMBER: Making prepin file for individual residues of huge molecule. (Mon Mar 21 2005 - 10:27:23 CST)
  • Re: AMBER: lmanal input file problem (Fri Mar 18 2005 - 14:10:00 CST)
  • Re: AMBER: Minimization of avg structure-SANDER Bomb (Thu Mar 17 2005 - 12:54:18 CST)
  • Re: AMBER: Minimization of avg structure-SANDER Bomb (Thu Mar 17 2005 - 10:51:59 CST)
  • Re: AMBER: Bus error - ambpdb (Thu Mar 17 2005 - 10:54:28 CST)
  • Re: AMBER: sander.QMMM and fcap (Thu Mar 17 2005 - 10:00:04 CST)
  • Re: AMBER: Hydrogen bonding question (Tue Mar 15 2005 - 09:23:30 CST)
  • Re: AMBER: spherical boundary condition (Sat Mar 12 2005 - 20:51:58 CST)
  • Re: AMBER: expected error in mean (Amber 8 TI tutorial) (Sat Mar 12 2005 - 16:18:40 CST)
  • Re: AMBER: PTRAJ $ Antechamber (Sat Mar 12 2005 - 16:17:49 CST)
  • Re: AMBER: IDIEL in sander (Sat Mar 12 2005 - 16:10:09 CST)
  • Re: AMBER: (Fri Mar 11 2005 - 13:02:40 CST)
  • Re: AMBER: radii "leap" from which file (Wed Mar 09 2005 - 19:02:43 CST)
  • Re: AMBER: solvatebox problem in the antechamber tutorial (Wed Mar 09 2005 - 18:18:19 CST)
  • Re: AMBER: vlimit in heating (Wed Mar 09 2005 - 10:10:42 CST)
  • Re: AMBER: Dummy atoms: Changing the source code (Tue Mar 08 2005 - 13:50:58 CST)
  • Re: AMBER: global pH variation in AMBER. (Tue Mar 08 2005 - 13:38:30 CST)
  • Re: AMBER: Energy fluctuations (Tue Mar 08 2005 - 13:36:14 CST)
  • Re: AMBER: New pmemd build utility; pathscale vs. pgi vs. ifort em64 opteron benchmarks (Mon Mar 07 2005 - 12:36:40 CST)
  • Re: AMBER: AMBER8 Compile Error on Dual Opteron (Sun Mar 06 2005 - 22:24:27 CST)
  • Re: AMBER: Citing Generalized Born Implicit solvent Model (igb=5) (Sun Mar 06 2005 - 19:14:35 CST)
  • Re: AMBER: Amber 8 on cygwin install problem (Sun Mar 06 2005 - 13:23:52 CST)
  • Re: AMBER: Antechamber/Divcon assigned charges (Thu Mar 03 2005 - 23:17:13 CST)
  • Re: AMBER: A problem about Gaussian (Thu Mar 03 2005 - 18:55:35 CST)
  • Re: AMBER: Installation problem (Thu Mar 03 2005 - 10:18:47 CST)
  • Re: AMBER: Amber 8 on cygwin install problem (Thu Mar 03 2005 - 10:07:52 CST)
  • Re: AMBER: bond type for a virtual bond in a biomolecular transition state (Wed Mar 02 2005 - 17:08:38 CST)
  • Re: AMBER: MM-GBSA (Wed Mar 02 2005 - 09:44:15 CST)
  • Re: AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem (Tue Mar 01 2005 - 10:41:08 CST)
  • Re: AMBER: Controlling number of water residues... (Tue Mar 01 2005 - 10:25:14 CST)
  • Re: AMBER: Amber8 Solaris installation failure (Mon Feb 28 2005 - 16:42:21 CST)
  • Re: AMBER: PDB conversion to gzmat using antechamber (Mon Feb 28 2005 - 12:02:58 CST)
  • Re: AMBER: GBSA calculation (Mon Feb 28 2005 - 11:48:24 CST)
  • Re: AMBER: vlimit problem (Mon Feb 28 2005 - 11:40:26 CST)
  • Re: AMBER: correlation (Mon Feb 28 2005 - 11:32:54 CST)
  • Re: AMBER: problem with solvateBox (Fri Feb 25 2005 - 15:41:38 CST)
  • Re: AMBER: ambpdb radii (Fri Feb 25 2005 - 12:15:57 CST)
  • Re: AMBER: make test.lmod error (Fri Feb 25 2005 - 11:41:32 CST)
  • Re: AMBER: solvateOct method (Fri Feb 25 2005 - 10:53:19 CST)
  • Re: AMBER: ambpdb radii (Fri Feb 25 2005 - 10:09:53 CST)
  • Re: AMBER: Does delta.charge mean "final charge" for a dummy atom? (Thu Feb 24 2005 - 20:31:04 CST)
  • Re: AMBER: ambpdb radii (Thu Feb 24 2005 - 18:56:40 CST)
  • Re: AMBER: Joining residues/units (Thu Feb 24 2005 - 14:54:37 CST)
  • Re: AMBER: Use of ibelly with nmode analysis (Thu Feb 24 2005 - 10:30:31 CST)
  • Re: AMBER: convert one functional group to another with TI (Wed Feb 23 2005 - 17:01:42 CST)
  • Re: AMBER: convert one functional group to another with TI (Wed Feb 23 2005 - 16:46:55 CST)
  • Re: AMBER: lastrst (Tue Feb 22 2005 - 23:53:28 CST)
  • Re: AMBER: convert one functional group to another with TI (Tue Feb 22 2005 - 23:44:41 CST)
  • Re: AMBER: total energy of solvation (Tue Feb 22 2005 - 23:40:47 CST)
  • Re: AMBER: Amber8 Solaris installation failure (Tue Feb 22 2005 - 18:52:13 CST)
  • Re: AMBER: Restraint of atoms during minimization (Tue Feb 22 2005 - 11:19:17 CST)
  • Re: AMBER: Formatting Questions (Mon Feb 21 2005 - 19:33:34 CST)
  • Re: AMBER: problem with protein minimization (Mon Feb 21 2005 - 18:11:37 CST)
  • Re: AMBER: AIX problem (Mon Feb 21 2005 - 18:05:40 CST)
  • Re: AMBER: Free energy extimate for the same structure but different conformers (Mon Feb 21 2005 - 18:00:39 CST)
  • Re: AMBER: DNA Tutorial (Mon Feb 21 2005 - 17:52:21 CST)
  • Re: AMBER: separate solvent-solvent and solvent-solute interaction (Mon Feb 21 2005 - 11:07:24 CST)
  • Re: AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) (Fri Feb 18 2005 - 01:56:20 CST)
  • Re: AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) (Fri Feb 18 2005 - 01:41:23 CST)
  • Re: AMBER: Amber8 Solaris installation failure (Thu Feb 17 2005 - 20:31:00 CST)
  • Re: AMBER: Amber7 nmropt (Wed Feb 16 2005 - 15:53:19 CST)
  • Re: AMBER: EWALD and belly not strictly correct (Wed Feb 16 2005 - 10:52:20 CST)
  • Re: AMBER: (Wed Feb 16 2005 - 10:49:18 CST)
  • AMBER: soft-cores and Amber (Tue Feb 15 2005 - 16:55:30 CST)
  • Re: AMBER: Dummy Atom Types on both states (Tue Feb 15 2005 - 16:26:21 CST)
  • Re: AMBER: check in leap (Tue Feb 15 2005 - 15:17:07 CST)
  • Re: AMBER: reverse TI charge perturbation (Sat Feb 12 2005 - 18:14:58 CST)
  • Re: AMBER: nucgen problem (Fri Feb 11 2005 - 19:37:32 CST)
  • Re: AMBER: inconsistent ordering in an improper dihedral of TRP (Fri Feb 11 2005 - 16:19:03 CST)
  • Re: AMBER: desc NEWRES and blank unit type (Fri Feb 11 2005 - 16:24:25 CST)
  • Re: AMBER: ptraj error and min problems (Fri Feb 11 2005 - 10:29:42 CST)
  • Re: AMBER: too much vacuum in the box created by Leap (Fri Feb 11 2005 - 10:21:29 CST)
  • Re: AMBER: Poisson Boltzmann dynamics error (Thu Feb 10 2005 - 10:57:51 CST)
  • Re: AMBER: question about surface area to GBsurf calculation (Thu Feb 10 2005 - 09:55:33 CST)
  • Re: AMBER: DIVCON optimization (Wed Feb 09 2005 - 20:22:07 CST)
  • Re: AMBER: DIVCON optimization (Wed Feb 09 2005 - 14:22:59 CST)
  • Re: AMBER: minimization.out (Wed Feb 09 2005 - 13:53:41 CST)
  • Re: AMBER: problem in minimization (Tue Feb 08 2005 - 16:23:51 CST)
  • Re: AMBER: Amber8 installation test possible failures (Tue Feb 08 2005 - 14:02:54 CST)
  • Re: AMBER: Linux Enterprise (Tue Feb 08 2005 - 13:59:15 CST)
  • Re: AMBER: problem in minimization (Tue Feb 08 2005 - 13:51:42 CST)
  • Re: AMBER: tleap load pdb file (Tue Feb 08 2005 - 13:50:08 CST)
  • Re: AMBER: MMGBSA and dielectric constant with AMBER8 - dielc and intdiel (Tue Feb 08 2005 - 13:28:23 CST)
  • Re: AMBER: problem in writing (Mon Feb 07 2005 - 17:22:05 CST)
  • Re: AMBER: Tutorial Request (Sun Feb 06 2005 - 11:40:28 CST)
  • Re: AMBER: loading pdb in leap to create parmeter files (Sat Feb 05 2005 - 16:29:13 CST)
  • Re: AMBER: Antechamber/formatting question (Sat Feb 05 2005 - 13:17:24 CST)
  • Re: AMBER: trajectory of minimization (Sat Feb 05 2005 - 12:54:39 CST)
  • Re: AMBER: Is droplet boundary condition option possible ? (Sat Feb 05 2005 - 12:53:53 CST)
  • Re: AMBER: huge bond distances in new residue (Sat Feb 05 2005 - 12:57:37 CST)
  • Re: AMBER: unnatural ligand (Fri Feb 04 2005 - 16:54:06 CST)
  • Re: AMBER: tleap load pdb file (Fri Feb 04 2005 - 16:45:50 CST)
  • Re: AMBER: dppsv returns error code: 29 (Fri Feb 04 2005 - 16:48:38 CST)
  • Re: AMBER: tleap load pdb file (Fri Feb 04 2005 - 10:35:49 CST)
  • Re: AMBER: protonate and input conversion error (Thu Feb 03 2005 - 12:09:31 CST)
  • Re: AMBER: gaff frcmod file for TI calculation (Wed Feb 02 2005 - 18:44:13 CST)
  • Re: AMBER: sander segmentation fault (Wed Feb 02 2005 - 16:39:06 CST)
  • Re: AMBER: sander segmentation fault (Wed Feb 02 2005 - 13:28:37 CST)
  • Re: AMBER: Multiple dihedral restraints (follow up) (Wed Feb 02 2005 - 13:04:47 CST)
  • Re: AMBER: change of prmtop file (Wed Feb 02 2005 - 12:21:34 CST)
  • Re: AMBER: External Electric Field (Wed Feb 02 2005 - 12:08:59 CST)
  • Re: AMBER: doubts with a new aminoacid (Tue Feb 01 2005 - 17:35:36 CST)
  • Re: AMBER: Multiple dihedral restraints (Tue Feb 01 2005 - 16:54:49 CST)
  • Re: AMBER: Carnal in Amber8 (Tue Feb 01 2005 - 11:27:25 CST)
  • Re: AMBER: Manuals need update: protonate -b and -c options gone in Amber 7 and 8 (Mon Jan 31 2005 - 16:56:21 CST)
  • Re: AMBER: FW: amber 8 problem (Mon Jan 31 2005 - 12:37:08 CST)
  • Re: AMBER: new tutorial available (Fri Jan 28 2005 - 18:57:28 CST)
  • Re: AMBER: antechamber error message (Fri Jan 28 2005 - 16:00:22 CST)
  • Re: AMBER: &dipoles in sander (Fri Jan 28 2005 - 12:21:59 CST)
  • Re: AMBER: TI with electrostatic decoupling at sander (Thu Jan 27 2005 - 19:27:10 CST)
  • Re: AMBER: ANTECHAMBER & DIVCON (Thu Jan 27 2005 - 19:12:23 CST)
  • Re: AMBER: TI with electrostatic decoupling at sander (Wed Jan 26 2005 - 23:51:32 CST)
  • Re: AMBER: new tutorial available (Wed Jan 26 2005 - 11:27:58 CST)
  • Re: AMBER: collision frequency in GBSA dynamics (Tue Jan 25 2005 - 16:23:34 CST)
  • Re: AMBER: NAN errors (Tue Jan 25 2005 - 16:09:11 CST)
  • Re: AMBER: Error while running resp. (Tue Jan 25 2005 - 10:43:32 CST)
  • Re: AMBER: TI with electrostatic decoupling at sander (Tue Jan 25 2005 - 10:41:36 CST)
  • Re: AMBER: How to make PDB file by myself (Tue Jan 25 2005 - 10:40:21 CST)
  • Re: AMBER: test suite possible failures (Mon Jan 24 2005 - 16:38:21 CST)
  • Re: AMBER: system size limit (Mon Jan 24 2005 - 00:56:30 CST)
  • Re: AMBER: Question about TI integral method (Mon Jan 24 2005 - 00:41:26 CST)
  • Re: AMBER: problem runing parallel (REM) on tru64 (Sat Jan 22 2005 - 12:25:55 CST)
  • Re: AMBER: eedmeth=5 (Sat Jan 22 2005 - 12:20:22 CST)
  • Re: AMBER: Andersen thermostat: target T? (Fri Jan 21 2005 - 18:23:17 CST)
  • Re: AMBER: amber 8 installation (Fri Jan 21 2005 - 11:55:50 CST)
  • Re: AMBER: Cutoff for anal (Thu Jan 20 2005 - 13:17:31 CST)
  • AMBER: new tutorial available (Thu Jan 20 2005 - 13:06:30 CST)
  • Re: AMBER: enhanced sampling methods (Wed Jan 19 2005 - 14:34:24 CST)
  • Re: AMBER: ptraj analysis (Wed Jan 19 2005 - 14:24:58 CST)
  • Re: AMBER: Scaling of charges in a polarizable simulation ! (Wed Jan 19 2005 - 14:11:08 CST)
  • Re: AMBER: Amber8 installation problems on Sparc/Solaris9 (Tue Jan 18 2005 - 10:48:33 CST)
  • Re: AMBER: details of new aminoacid (Tue Jan 18 2005 - 10:01:20 CST)
  • Re: AMBER: new aminoacid (Mon Jan 17 2005 - 11:56:34 CST)
  • Re: AMBER: protonate (Fri Jan 14 2005 - 12:36:35 CST)
  • Re: AMBER: units (Wed Jan 12 2005 - 11:22:03 CST)
  • Re: AMBER: PB dynamics (Wed Jan 12 2005 - 11:26:19 CST)
  • Re: AMBER: Dummy Atoms: How to create them? (Tue Jan 11 2005 - 23:54:02 CST)
  • Re: AMBER: AMBER tutorial ambpdb question (Mon Jan 10 2005 - 21:16:10 CST)
  • Re: AMBER: dynamics (Sat Jan 08 2005 - 15:05:53 CST)
  • Re: AMBER: Weighting of different restraint types? (Fri Jan 07 2005 - 18:06:37 CST)
  • Re: AMBER: recompiling problem on IBM aix (Fri Jan 07 2005 - 13:03:30 CST)
  • Re: AMBER: about install amber8 on windows (Fri Jan 07 2005 - 12:59:27 CST)
  • Re: AMBER: How can i use AMBER with CHARMM forcefield parameter? (Thu Jan 06 2005 - 08:23:44 CST)
  • Re: AMBER: Dummy Atoms: How to create them? (Wed Jan 05 2005 - 11:40:11 CST)
  • Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied (Mon Jan 03 2005 - 10:34:09 CST)
  • Re: AMBER: Sander and NMODE energy minimization (Sun Jan 02 2005 - 16:47:28 CST)
  • Re: AMBER: NSCM (Sun Jan 02 2005 - 16:35:54 CST)
• David Bevan
  • Re: AMBER: Making movie from AMBER trajectory (Mon Nov 07 2005 - 12:50:19 CST)
• David C. Chan
  • AMBER: Bus error - ambpdb (Thu Mar 17 2005 - 08:54:17 CST)
• David Caliga
  • AMBER: Build for single precision (Thu Dec 15 2005 - 09:31:02 CST)
• David Case
  • Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth (Thu Apr 28 2005 - 08:03:00 CDT)
  • Re: AMBER: langevin, GB and simulated annealing - 4 (Tue Apr 26 2005 - 10:44:32 CDT)
  • Re: AMBER: AMBER Test (Tue Apr 26 2005 - 09:12:05 CDT)
  • Re: AMBER: langevin, GB and simulated annealing - 3 (Tue Apr 26 2005 - 09:06:08 CDT)
• David Cowburn
  • RE: AMBER: About Salt concentration (Wed Dec 21 2005 - 15:33:15 CST)
• David E. Konerding
  • Re: AMBER: ptraj crash error (Fri Dec 02 2005 - 12:24:35 CST)
  • Re: AMBER: Making movie from AMBER trajectory using UCSF Chimera (Wed Nov 09 2005 - 10:21:29 CST)
  • Re: AMBER: Making movie from AMBER trajectory (Tue Nov 08 2005 - 17:01:13 CST)
  • Re: AMBER: Making movie from AMBER trajectory (Tue Nov 08 2005 - 12:56:55 CST)
  • Re: AMBER: Steered Molecular Dynamics with AMBER? (Tue Jan 04 2005 - 22:44:15 CST)
• David E. Konerding DSD staff
  • Re: AMBER: generate charmm paramater file from amber parm file (Wed Feb 16 2005 - 12:13:23 CST)
  • Re: AMBER: problems with running sander in parallel on linux (Tue Feb 15 2005 - 14:48:50 CST)
• David LeBard
  • Re: AMBER: residence time of electrons/holes in DNA (Wed Aug 17 2005 - 18:43:47 CDT)
  • RE: Re: AMBER: a trivial question (Fri Aug 05 2005 - 11:32:47 CDT)
  • Re: AMBER: power supply crash==>boot problems (Wed Aug 03 2005 - 12:20:30 CDT)
  • Re: AMBER: pdb files from traj file (Wed Jul 13 2005 - 16:30:07 CDT)
  • Re: AMBER: Water simulation (Sat Jul 09 2005 - 19:30:55 CDT)
  • AMBER: Water simulation (Fri Jul 08 2005 - 18:44:12 CDT)
  • Re: AMBER: problem with addIons (Wed Jul 06 2005 - 17:08:35 CDT)
  • Re: AMBER: dielectric constant (Tue Jun 28 2005 - 15:01:30 CDT)
  • Re: AMBER: compiler (Tue Jun 14 2005 - 12:45:27 CDT)
  • Re: AMBER: Sander/Mpich2 error with mpd_singinit (Thu Apr 14 2005 - 15:17:54 CDT)
• David Mathews
  • Re: AMBER: installation of amber 8 on windows (Sat Feb 19 2005 - 10:01:54 CST)
  • Re: AMBER: installation of amber 8 on windows (Thu Feb 17 2005 - 10:42:05 CST)
• David Mobley
  • Re: AMBER: more data points on the parmchk problem (Wed Nov 30 2005 - 11:04:01 CST)
  • AMBER: rdparm bug (Tue Nov 29 2005 - 20:40:02 CST)
  • Re: AMBER: constant pressure vs. constant volume heating (Tue Nov 29 2005 - 13:20:46 CST)
  • Re: AMBER: some problems with Antechamber (Tue Nov 29 2005 - 13:08:00 CST)
  • AMBER: some problems with Antechamber (Tue Nov 29 2005 - 10:39:26 CST)
  • Re: AMBER: antechamber -- missing improper torsions (Fri Oct 21 2005 - 12:21:01 CDT)
  • Re: AMBER: antechamber -- missing improper torsions (Tue Oct 18 2005 - 14:21:39 CDT)
  • AMBER: antechamber -- missing improper torsions (Mon Oct 17 2005 - 13:33:43 CDT)
  • AMBER: antechamber -- missing improper torsions (Wed Sep 28 2005 - 17:35:25 CDT)
  • Re: AMBER: Amber 8: questions about free energy perturbation (Fri Sep 23 2005 - 14:40:03 CDT)
  • AMBER: ibelly and free energy calculations (Mon Sep 12 2005 - 16:36:25 CDT)
  • Re: AMBER: Error: vlimit exceeded for step (Tue May 24 2005 - 14:27:23 CDT)
• david.evans_at_ulsop.ac.uk
  • Re: AMBER: Compiling just sander (Fri Mar 11 2005 - 03:24:24 CST)
  • Re: AMBER: nmode entropy calculations in MMPBSA (Fri Feb 25 2005 - 08:14:55 CST)
  • Re: AMBER: generate charmm paramater file from amber parm file (Wed Feb 16 2005 - 12:02:07 CST)
  • Re: AMBER: Dummy Atom Types on both states (Tue Feb 15 2005 - 12:13:57 CST)
  • Re: AMBER: Dummy Atom Types on both states (Tue Feb 15 2005 - 11:29:39 CST)
  • Re: AMBER: calculating electrostatic potential (Tue Jan 25 2005 - 05:24:52 CST)
• David.LeBard_at_asu.edu
  • AMBER: Energy fluctuations (Tue Mar 08 2005 - 11:40:46 CST)
• David.Maxwell_at_di.mdacc.tmc.edu
  • AMBER: Strange difference in speed between Altix (Itanium2) and Tezro (MIPS) SGI for small GB/SA run (Wed Aug 03 2005 - 12:39:43 CDT)
  • AMBER: LCPO SASA parameters for other elements when using gbsa=1 option (Fri Jul 08 2005 - 15:10:00 CDT)
  • AMBER: Problems with Iodine (Fri Mar 18 2005 - 15:03:38 CST)
• Dawei Zhang
  • Re: AMBER: P4 EM64T Intel Fortran Compile Problem (Fri Jul 15 2005 - 15:54:39 CDT)
  • AMBER: P4 EM64T Intel Fortran Compile Problem (Fri Jul 15 2005 - 12:04:49 CDT)
  • AMBER: ibelly in nmode (Thu May 05 2005 - 14:23:13 CDT)
• Delon Wilson
  • AMBER: RESP charges with Gaussian03 and Amber (Mon Apr 18 2005 - 08:19:16 CDT)
  • AMBER: RESP charges with Gaussian03 and Amber (Fri Apr 15 2005 - 15:57:19 CDT)
• Devashish Kumar
  • AMBER: Comparison of AMBER against DL-POLY (Tue Jul 12 2005 - 17:32:03 CDT)
• Difei Wang
  • Re: AMBER: new tutorial available (Fri Jan 28 2005 - 18:08:59 CST)
• dkohen_at_carleton.edu
  • AMBER: amber 8 system requirements (Wed Feb 02 2005 - 12:28:48 CST)
• dmcelh_at_uchicago.edu
  • Fwd: AMBER: rdc multiple tensors (Tue Dec 20 2005 - 11:55:51 CST)
  • AMBER: rdc multiple tensors (Mon Dec 19 2005 - 17:01:13 CST)
• dmitri.mikhailov_at_novartis.com
  • AMBER: antechamber availability (Wed Mar 23 2005 - 14:40:47 CST)
• Don.Bashford_at_stjude.org
  • Re: AMBER: How to add water to calculate MMPBSA. . (Thu Dec 15 2005 - 11:13:30 CST)
  • Re: AMBER: Mg2+ issues of using MM-PB/GBSA. . (Mon Dec 05 2005 - 12:09:20 CST)
  • Re: AMBER: Installation problem. . (Mon Jun 13 2005 - 12:56:46 CDT)
• Donald Thomas
  • AMBER: Using RED to calculate partial charges of new amino acid (Tue Oct 25 2005 - 09:50:40 CDT)
• Douali, Latifa
  • AMBER: rotational motion in periodic simulation (Fri Dec 02 2005 - 12:50:28 CST)
  • FW: AMBER: number of processors (Thu Sep 29 2005 - 15:49:29 CDT)
  • RE: AMBER: number of processors (Wed Sep 28 2005 - 12:41:21 CDT)
  • AMBER: AMBBER: ptraj question (Fri Sep 09 2005 - 15:49:24 CDT)
  • RE: AMBER: new residue (Wed Jul 27 2005 - 16:36:27 CDT)
  • RE: AMBER: new residue (Wed Jul 27 2005 - 15:45:17 CDT)
  • RE: AMBER: new residue (Wed Jul 27 2005 - 11:09:01 CDT)
  • AMBER: new residue (Tue Jul 26 2005 - 19:50:51 CDT)
  • FW: AMBER: TI - frcmod file (Wed Jul 13 2005 - 10:38:25 CDT)
  • AMBER: Create new Unit (Thu Jun 30 2005 - 18:45:37 CDT)
  • AMBER: inpcrd file (Fri Jun 10 2005 - 18:04:24 CDT)
  • AMBER:Sander errors: Unit 6 Error on OPEN: mdout (Tue May 31 2005 - 12:34:41 CDT)
• drugdesign
  • AMBER: question about sander minimization error (Thu Jul 07 2005 - 03:37:51 CDT)
  • AMBER: stack terminated abnormally (Tue May 31 2005 - 05:20:33 CDT)
• dthomas_at_chem.uwa.edu.au
  • AMBER: nucgen and nukit (Tue Jul 05 2005 - 09:55:44 CDT)
• du yongchun
  • AMBER: some questions when using ATP (Wed Oct 26 2005 - 21:28:44 CDT)
  • AMBER: question whem using leap (Thu Jun 02 2005 - 02:25:16 CDT)
  • AMBER: amber question about leap (Thu Jun 02 2005 - 00:12:12 CDT)
• duan_list_at_albert.genomecenter.ucdavis.edu
  • Re: AMBER: a bimolecular reaction (Tue Apr 12 2005 - 13:00:14 CDT)
  • Re: AMBER: nscm (Tue Apr 12 2005 - 11:45:49 CDT)
  • Re: AMBER: About Gaussian Key Words (fwd) (Thu Apr 07 2005 - 18:09:25 CDT)
• Dustin
  • AMBER: antechamber (Mon Jul 25 2005 - 15:30:40 CDT)
  • AMBER: Trouble with Amber8 (Tue Jul 19 2005 - 15:16:10 CDT)
• Dwayne Hoobler
  • RE: AMBER: DNA Tutorial (Mon Feb 21 2005 - 14:26:37 CST)
  • AMBER: DNA Tutorial (Fri Feb 18 2005 - 17:07:34 CST)
• E.A.Moore
  • AMBER: 6-thioguanine (Tue Dec 06 2005 - 08:31:59 CST)
  • AMBER: Parameters for S-substituted nucleic acids (Thu Nov 24 2005 - 03:29:18 CST)
• Ed Pate
  • AMBER: distance restraint simulation (Tue Dec 27 2005 - 12:36:44 CST)
  • AMBER: distance restraints (Sat Dec 17 2005 - 16:43:32 CST)
  • AMBER: question about initial conditions for amber (Sun May 29 2005 - 21:42:21 CDT)
  • AMBER: problem with belly calculation restart (Thu Apr 21 2005 - 19:28:59 CDT)
  • Re: AMBER: carnal problem (Fri Apr 15 2005 - 14:30:26 CDT)
  • Re: AMBER: carnal problem (Fri Apr 15 2005 - 13:53:37 CDT)
  • Re: AMBER: carnal problem (Fri Apr 15 2005 - 13:10:37 CDT)
  • AMBER: carnal problem (Fri Apr 15 2005 - 11:15:54 CDT)
• emilia wu
  • AMBER: mm_pbsa problem (Mon Oct 31 2005 - 20:53:51 CST)
  • AMBER: average structure (Sun Jun 19 2005 - 19:15:53 CDT)
  • Re: RE: AMBER: problem with gb md (Fri May 06 2005 - 01:29:33 CDT)
  • AMBER: problem with gb md (Thu May 05 2005 - 21:05:00 CDT)
  • AMBER: (Wed Apr 27 2005 - 21:35:59 CDT)
  • Re: RE: Re: AMBER: (Tue Apr 05 2005 - 07:25:42 CDT)
  • Re: Re: AMBER: (Tue Apr 05 2005 - 01:43:49 CDT)
  • AMBER: (Mon Apr 04 2005 - 09:11:48 CDT)
• Emmanuel Giudice
  • Re: AMBER: Compiling AMBER 8 for Mac OSX (Parallel) (Tue Jan 18 2005 - 00:09:47 CST)
• Eric Hu
  • Re: AMBER: lib file for nonstandard residue (Thu Jul 14 2005 - 17:02:35 CDT)
  • AMBER: lib file for nonstandard residue (Wed Jul 13 2005 - 18:52:19 CDT)
  • AMBER: normal mode mm/pbsa interupted (Thu Jun 09 2005 - 13:46:04 CDT)
  • Re: AMBER: mm/pbsa error (Wed Jun 01 2005 - 12:23:53 CDT)
  • AMBER: mm/pbsa error (Wed May 04 2005 - 13:06:34 CDT)
  • Re: AMBER: big fluctuation in MM-PBSA/GA (Fri Apr 15 2005 - 16:42:45 CDT)
  • Re: AMBER: big fluctuation in MM-PBSA/GA (Fri Apr 15 2005 - 13:59:09 CDT)
  • Re: AMBER: big fluctuation in MM-PBSA/GA (Thu Apr 14 2005 - 19:21:40 CDT)
  • AMBER: big fluctuation in MM-PBSA/GA (Thu Apr 14 2005 - 17:54:05 CDT)
  • Re: AMBER: small target pressure in constant pressure dynamics (Thu Apr 14 2005 - 17:26:23 CDT)
  • AMBER: small target pressure in constant pressure dynamics (Thu Apr 14 2005 - 16:37:49 CDT)
  • Re: AMBER: a bimolecular reaction (Wed Apr 13 2005 - 13:08:03 CDT)
  • Re: AMBER: a bimolecular reaction (Tue Apr 12 2005 - 18:50:58 CDT)
  • AMBER: a bimolecular reaction (Wed Apr 06 2005 - 12:14:23 CDT)
  • Re: AMBER: OH- dynamics (Wed Mar 30 2005 - 18:23:32 CST)
  • Re: AMBER: OH- dynamics (Wed Mar 30 2005 - 16:50:03 CST)
  • Re: AMBER: OH- dynamics (Wed Mar 30 2005 - 16:03:53 CST)
  • AMBER: OH- dynamics (Wed Mar 30 2005 - 11:55:19 CST)
  • AMBER: mm-pbsa with multiple-processors (Mon Mar 21 2005 - 16:21:16 CST)
  • AMBER: substrate exit from protein in Amber 8.0 TI vdw simulation (Fri Mar 18 2005 - 17:35:39 CST)
  • AMBER: expected error in mean (Amber 8 TI tutorial) (Thu Mar 10 2005 - 17:38:13 CST)
  • Re: AMBER: bond connectivity among dummy atoms (Thu Mar 03 2005 - 16:12:26 CST)
  • Re: AMBER: bond connectivity among dummy atoms (Thu Mar 03 2005 - 15:25:19 CST)
  • AMBER: bond connectivity among dummy atoms (Thu Mar 03 2005 - 12:56:32 CST)
  • AMBER: bond type for a virtual bond in a biomolecular transition state (Wed Mar 02 2005 - 16:54:45 CST)
  • Re: AMBER: Does delta.charge mean "final charge" for a dummy atom? (Fri Feb 25 2005 - 18:38:05 CST)
  • AMBER: Does delta.charge mean "final charge" for a dummy atom? (Thu Feb 24 2005 - 19:22:23 CST)
  • Re: AMBER: convert one functional group to another with TI (Wed Feb 23 2005 - 17:18:29 CST)
  • Re: AMBER: convert one functional group to another with TI (Wed Feb 23 2005 - 00:36:03 CST)
  • AMBER: convert one functional group to another with TI (Tue Feb 22 2005 - 19:29:42 CST)
  • Re: AMBER: reverse TI charge perturbation (Mon Feb 14 2005 - 18:42:14 CST)
  • AMBER: reverse TI charge perturbation (Fri Feb 11 2005 - 19:59:10 CST)
  • AMBER: minimize a ptraj average pdb structure (Tue Feb 08 2005 - 19:48:26 CST)
  • Re: AMBER: unnatural ligand (Mon Feb 07 2005 - 12:28:14 CST)
  • AMBER: unnatural ligand (Thu Feb 03 2005 - 21:37:41 CST)
  • Re: AMBER: gaff frcmod file for TI calculation (Wed Feb 02 2005 - 19:47:32 CST)
  • AMBER: gaff frcmod file for TI calculation (Wed Feb 02 2005 - 17:50:00 CST)
  • Re: AMBER: skip snapshots with ptraj in amber 8.0 (Mon Jan 31 2005 - 19:08:26 CST)
  • AMBER: skip snapshots with ptraj in amber 8.0 (Mon Jan 31 2005 - 13:30:58 CST)
• Eric Mullins
  • AMBER: FW: Amber installation (Wed Apr 06 2005 - 10:36:20 CDT)
• Eric Pettersen
  • Re: AMBER: recent Chimera MD enhancements (Tue Nov 15 2005 - 15:09:21 CST)
  • AMBER: recent Chimera MD enhancements (Tue Nov 15 2005 - 14:59:16 CST)
• Eugene Billiot
  • AMBER: building amino acid based surfactants? (Mon Dec 26 2005 - 15:25:33 CST)
• Eugene DeRose
  • AMBER: GB refinement of CYANA structures (Fri Sep 16 2005 - 08:25:52 CDT)
• Fabian Boes
  • Re: AMBER: INTRA molecular hbonds (Mon Jun 27 2005 - 09:45:13 CDT)
  • Re: AMBER: Hbond analysis (Mon Jun 27 2005 - 08:12:34 CDT)
• Fabien Cailliez
  • AMBER: cut-offs in non-periodic simulations (Mon Oct 03 2005 - 11:31:26 CDT)
  • AMBER: masks in ptraj - Hbond analysis (Tue Sep 06 2005 - 06:38:11 CDT)
  • AMBER: cap and ptraj (Tue Jul 19 2005 - 17:14:50 CDT)
  • AMBER: cap simulations questions (Mon Jul 18 2005 - 09:50:32 CDT)
  • AMBER: problems with bonds in sander (Thu Jul 07 2005 - 13:18:19 CDT)
  • AMBER: questions about topology file (Fri Jul 01 2005 - 10:49:20 CDT)
  • AMBER: 10-12 potential and create atom type (Thu Jun 30 2005 - 12:19:41 CDT)
  • Re: AMBER: distance restraints between two centers of mass (Thu May 26 2005 - 04:01:08 CDT)
  • AMBER: strange VDWAALS and EEL energies calculated by pbsa (Fri Apr 22 2005 - 10:56:41 CDT)
  • AMBER: Warning: Error opening "New" file from subroutine OPNMRG in pmemd (Thu Apr 14 2005 - 08:05:32 CDT)
  • Re: AMBER: MM_PBSA problem (Tue Apr 12 2005 - 11:50:14 CDT)
  • AMBER: linit in mm-pbsa (Fri Apr 08 2005 - 04:08:52 CDT)
  • AMBER: RADIOPT=1 (Thu Apr 07 2005 - 08:19:09 CDT)
  • AMBER: warning in PBSA (Wed Mar 23 2005 - 07:39:00 CST)
  • AMBER: add waters to a system + leap problem with solvateOct command (Thu Mar 17 2005 - 12:30:24 CST)
  • AMBER: nmode entropy calculations in MMPBSA (Fri Feb 25 2005 - 04:20:23 CST)
  • Re: AMBER: size of solventbox (Wed Feb 23 2005 - 05:21:52 CST)
  • Re: AMBER: problem with ptraj and randomizeions (Fri Feb 18 2005 - 02:50:00 CST)
  • AMBER: problem with ptraj and randomizeions (Thu Feb 17 2005 - 11:56:24 CST)
  • AMBER: MMGBSA and dielectric constant with AMBER8 - dielc and intdiel (Tue Feb 08 2005 - 11:16:51 CST)
  • Re: AMBER: pmemd and restraints (Thu Jan 27 2005 - 03:01:31 CST)
  • AMBER: pmemd and distance restraint (Thu Jan 20 2005 - 04:39:20 CST)
  • AMBER: GB differences between AMBER7 and AMBER8 (Tue Jan 18 2005 - 07:53:04 CST)
  • Re: AMBER: distance restraint and file fort.35 (Mon Jan 17 2005 - 09:58:03 CST)
  • AMBER: distance restraint and file fort.35 (Mon Jan 17 2005 - 05:34:00 CST)
• Fajar Rakhman Wibowo
  • Re: AMBER: transfer data from Linux to windows (Thu Jun 09 2005 - 18:11:33 CDT)
• fangyu liang
  • Re: AMBER: fast 1/r methods (Mon May 02 2005 - 09:17:32 CDT)
  • AMBER: Sander and NMODE energy minimization (Sat Jan 01 2005 - 23:53:49 CST)
• Filip Lankas
  • Re: AMBER: problem with ptraj and randomizeions (Fri Feb 18 2005 - 06:19:10 CST)
  • AMBER: stereo (Wed Feb 09 2005 - 11:53:45 CST)
  • AMBER: pmemd and restraints (Wed Jan 26 2005 - 11:01:50 CST)
• Florian Barth
  • Re: AMBER: PMEMD with big systems (Wed Mar 23 2005 - 14:48:10 CST)
  • AMBER: PMEMD with big systems (Fri Mar 18 2005 - 17:25:41 CST)
• Freeman William
  • We can send you disccounted errection mads party (Thu May 12 2005 - 00:23:35 CDT)
• Furse, Kristina Elisabet
  • RE: AMBER: Leap handling crystallographic waters (Tue Nov 22 2005 - 13:18:34 CST)
  • Re: AMBER: Leap handling crystallographic waters (Tue Nov 22 2005 - 11:13:57 CST)
  • Re: AMBER: Using OPLS atom types (Tue Nov 22 2005 - 11:10:06 CST)
  • Re: AMBER: Simple 3D Molecule Visualization (Tue Oct 18 2005 - 17:10:54 CDT)
  • Re: AMBER: new residue (Tue Jul 26 2005 - 20:40:51 CDT)
  • Re: AMBER: Leap problem (Thu Jul 14 2005 - 19:31:40 CDT)
  • Re: AMBER: Ptraj and order of operations (Wed Jul 13 2005 - 13:55:02 CDT)
  • Re: AMBER: Ptraj and order of operations (Tue Jul 12 2005 - 20:07:04 CDT)
  • AMBER: Ptraj and order of operations (Mon Jul 11 2005 - 19:26:09 CDT)
  • Re: AMBER: nmropt =1 AND ntr=1 in pmemd (Fri Jun 17 2005 - 14:16:13 CDT)
  • Re: AMBER: crashing xleap (Fri May 20 2005 - 17:28:05 CDT)
  • Re: AMBER: read pdb back to xleap after solvation of chloroform (Fri May 20 2005 - 16:20:55 CDT)
  • Re: AMBER: Formatting a restraint file (Thu Apr 14 2005 - 15:02:20 CDT)
  • Re: AMBER: Formatting a restraint file (Thu Apr 14 2005 - 00:06:49 CDT)
  • Re: AMBER: rst file problems (Tue Apr 12 2005 - 15:39:35 CDT)
  • Re: AMBER: lastrst (Wed Feb 23 2005 - 15:36:08 CST)
  • Re: AMBER: sander segmentation fault (Wed Feb 02 2005 - 17:32:25 CST)
  • Re: AMBER: Problem in ptraj (Wed Feb 02 2005 - 12:16:03 CST)
  • Re: AMBER: Problem in ptraj (Tue Feb 01 2005 - 13:30:53 CST)
  • Re: AMBER: Problem in ptraj (Mon Jan 31 2005 - 11:22:21 CST)
  • Re: AMBER: IGB parameter (Wed Jan 19 2005 - 13:33:13 CST)
• FyD
  • AMBER: Relax in tLEaP ? (Wed Dec 07 2005 - 08:00:38 CST)
  • Re: AMBER: RESP: Question (Tue Dec 06 2005 - 07:13:49 CST)
  • Re: AMBER: RESP: Question (Mon Dec 05 2005 - 15:31:32 CST)
  • Re: AMBER: reordering atoms after antechamber (Mon Nov 28 2005 - 09:10:17 CST)
  • Re: AMBER: RED: extra variable definition (Tue Nov 22 2005 - 03:40:09 CST)
  • Re: AMBER: RED: extra variable definition (Tue Nov 22 2005 - 03:34:33 CST)
  • Re: AMBER: RED: extra variable definition (Mon Nov 21 2005 - 08:58:17 CST)
  • Re: AMBER: Question about PDB format (Sun Nov 20 2005 - 08:21:22 CST)
  • AMBER: Question about PDB format (Sat Nov 19 2005 - 02:11:23 CST)
  • AMBER: RED and EP from GAMESS (Fri Nov 18 2005 - 06:04:47 CST)
  • Re: AMBER: RESP problem RESP (Mon Nov 14 2005 - 08:59:12 CST)
  • Re: AMBER: Resp install problem, again (Thu Nov 10 2005 - 15:49:21 CST)
  • Re: AMBER: XRED II error while initializing (Wed Nov 09 2005 - 02:06:58 CST)
  • Re: AMBER: XRED II error while initializing (Mon Nov 07 2005 - 07:03:05 CST)
  • Re: AMBER: Density of Cyclohexane box (Thu Nov 03 2005 - 01:47:41 CST)
  • Re: AMBER: seg fault error in resp (Thu Oct 27 2005 - 09:39:44 CDT)
  • Re: AMBER: seg fault error in resp (Wed Oct 26 2005 - 11:13:05 CDT)
  • Re: AMBER: seg fault error in resp (Wed Oct 26 2005 - 09:06:40 CDT)
  • Re: AMBER: Using RED to calculate partial charges of new amino acid (Wed Oct 26 2005 - 05:36:21 CDT)
  • Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED (Tue Oct 25 2005 - 00:58:56 CDT)
  • Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED (Mon Oct 24 2005 - 03:44:31 CDT)
  • Re: AMBER: Simulating transition metals in amber (Mon Oct 24 2005 - 03:21:52 CDT)
  • Re: Problem solved! Re: AMBER: How to get PDB structures optimized for RED-II (Mon Oct 24 2005 - 03:27:07 CDT)
  • Re: AMBER: Neutral C-terminal residue (Wed Oct 19 2005 - 07:17:12 CDT)
  • Re: AMBER: Simple 3D Molecule Visualization (Tue Oct 18 2005 - 14:16:19 CDT)
  • RE: AMBER: Scaling factor of NMR restraint (Sat Oct 15 2005 - 01:34:58 CDT)
  • AMBER: Scaling factor of NMR restraint (Fri Oct 14 2005 - 09:28:24 CDT)
  • Re: AMBER: Modified RNA Bases (Tue Sep 27 2005 - 00:45:17 CDT)
  • Re: AMBER: D-enantiomers (Fri Sep 23 2005 - 02:12:36 CDT)
  • Re: AMBER: D-enantiomers (Thu Sep 22 2005 - 07:15:49 CDT)
  • Re: AMBER: D-enantiomers (Thu Sep 22 2005 - 02:03:55 CDT)
  • Re: AMBER: D-enantiomers (Wed Sep 21 2005 - 01:53:49 CDT)
  • Re: AMBER: creating a resp input file without Gaussian. (Tue Sep 20 2005 - 01:47:20 CDT)
  • AMBER: New information about AmberFFC (Wed Sep 14 2005 - 05:18:36 CDT)
  • Re: AMBER: Quick question about xLeap (Thu Sep 08 2005 - 09:54:12 CDT)
  • Re: AMBER: How to get PDB structures optimized for RED-II (Wed Sep 07 2005 - 07:40:25 CDT)
  • Re: AMBER: RED and Multi-Orientation (Wed Sep 07 2005 - 06:29:54 CDT)
  • Re: AMBER: generation of conformations for multi-conf. RESP fitting (Tue Sep 06 2005 - 11:20:52 CDT)
  • Re: AMBER: How to get PDB structures optimized for RED-II (Tue Sep 06 2005 - 04:36:51 CDT)
  • Re: AMBER: RED-II failure to recognize GAMESS output (Tue Sep 06 2005 - 03:48:41 CDT)
  • Re: AMBER: RED and Multi-Orientation (Tue Sep 06 2005 - 02:35:58 CDT)
  • Re: AMBER: RED-II failure to recognize GAMESS output (Sat Sep 03 2005 - 02:33:38 CDT)
  • Re: AMBER: RED II and Gaussian (Sat Aug 27 2005 - 10:02:09 CDT)
  • AMBER: Release of R.E.D-II (Thu Jul 07 2005 - 12:58:54 CDT)
  • Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends (Thu Jul 07 2005 - 10:54:00 CDT)
  • Re: AMBER: please help us on partial charge calculation of PT complex using RESP (Fri Jul 01 2005 - 11:07:40 CDT)
  • Re: AMBER: Create new Unit (Thu Jun 30 2005 - 19:25:02 CDT)
  • Re: AMBER: RED question (Wed Jun 29 2005 - 11:34:16 CDT)
  • Re: AMBER: RED question (Sun Jun 26 2005 - 22:37:59 CDT)
  • Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends (Wed Jun 22 2005 - 16:56:30 CDT)
  • Re: AMBER: Request for g98 (IOP...) (Tue Jun 14 2005 - 10:55:27 CDT)
  • Re: AMBER: Need help in charge fitting through RESP (Mon Jun 13 2005 - 11:15:42 CDT)
  • Re: AMBER: RESP charge fitting for N-methylguanine cation (Fri May 13 2005 - 10:33:05 CDT)
  • Re: AMBER: creating residues - charge assign problems (Fri May 13 2005 - 10:25:48 CDT)
  • Re: AMBER: Problem with xleap (Wed May 11 2005 - 21:21:12 CDT)
  • Re: AMBER: Asking how to creat alanine "dipeptide" in amber8 (Wed May 11 2005 - 11:06:27 CDT)
  • Re: AMBER: Re: R.E.D. question (Mon May 02 2005 - 14:53:35 CDT)
  • AMBER: Re: R.E.D. question (Fri Apr 29 2005 - 15:21:34 CDT)
  • Re: AMBER: capping (Thu Apr 28 2005 - 11:21:03 CDT)
  • Re: AMBER: capping (Wed Apr 27 2005 - 11:40:36 CDT)
  • Re: AMBER: How to deal with the Non-standard residue (Mon Apr 25 2005 - 15:07:33 CDT)
  • Re: AMBER: RESP charges - multiple conformations (Tue Apr 19 2005 - 09:26:48 CDT)
  • Re: AMBER: RESP charges - multiple conformations (Tue Apr 19 2005 - 00:44:04 CDT)
  • Re: AMBER: RESP charges with Gaussian03 and Amber (Fri Apr 15 2005 - 17:16:05 CDT)
  • Re: AMBER: Antechamber -reorders atom sequence (Fri Apr 15 2005 - 11:10:27 CDT)
  • Re: AMBER: Disulfide bond (Fri Apr 08 2005 - 11:09:03 CDT)
  • Re: AMBER: how to get the parameters for modified amino acid residue? (Fri Apr 08 2005 - 11:03:34 CDT)
  • AMBER: Re: ask for your help: parallel on mm_pbsa (Sat Mar 26 2005 - 11:09:23 CST)
  • Re: AMBER: Methionine with both C-ter and N-ter (Tue Mar 22 2005 - 18:26:35 CST)
  • Re: AMBER: mm-pbsa with multiple-processors (Mon Mar 21 2005 - 16:39:54 CST)
  • Re: AMBER: Cu++ and RED (Sat Mar 12 2005 - 16:00:56 CST)
  • Re: AMBER: Cu++ and RED (Sat Mar 12 2005 - 11:35:53 CST)
  • RE: AMBER: capping? (Wed Mar 09 2005 - 10:51:32 CST)
  • Re: AMBER: R.E.D (Sun Mar 06 2005 - 19:42:20 CST)
  • Re: AMBER: A problem about Gaussian (Thu Mar 03 2005 - 17:27:23 CST)
  • Re: AMBER: phosphorylated DNA not recognized (Thu Mar 03 2005 - 12:59:27 CST)
  • Re: AMBER: An error during minimization using RED (Tue Mar 01 2005 - 15:44:33 CST)
  • Re: AMBER: Antechamber/formatting question (Sun Feb 27 2005 - 22:43:23 CST)
  • Re: AMBER: Antechamber/formatting question (Sun Feb 27 2005 - 22:12:37 CST)
  • Re: AMBER: Joining residues/units (Fri Feb 25 2005 - 11:13:29 CST)
  • Re: AMBER: Cu++ and RED (Tue Feb 15 2005 - 12:19:16 CST)
  • Re: AMBER: Cu++ and RED (Fri Feb 11 2005 - 11:23:53 CST)
  • Re: AMBER: Creating an input file for GRASP using AMBER 8 (Mon Feb 07 2005 - 16:45:05 CST)
  • Re: AMBER: Creating an input file for GRASP using AMBER 8 (Mon Feb 07 2005 - 13:52:42 CST)
  • Re: AMBER: D-amino acid prep-files(simple method) (Sun Jan 23 2005 - 14:05:38 CST)
  • Re: AMBER: Problem with computing Resp charges using RED (Sat Jan 01 2005 - 13:51:12 CST)
• Garhan Attebury
  • AMBER: Sander Restart Problem (Tue May 24 2005 - 10:07:49 CDT)
  • Re: AMBER: generating over 16 bps of DNA in nucgen (Tue May 17 2005 - 10:27:13 CDT)
• george Chen
  • Re: AMBER: How to fix the atom in NPT case? (Tue May 03 2005 - 15:50:59 CDT)
  • Re: AMBER: How to fix the atom in NPT case? (Mon May 02 2005 - 14:35:42 CDT)
  • AMBER: How to fix the atom in NPT case? (Mon May 02 2005 - 13:19:54 CDT)
• Germán Sciaini
  • AMBER: hi (Wed Dec 07 2005 - 04:51:06 CST)
  • Re: AMBER: Question about Lennard-Jones Parameters in Topology file (Mon Jul 04 2005 - 05:46:00 CDT)
  • Re: AMBER: cavity volume (Mon Jul 04 2005 - 05:29:59 CDT)
  • AMBER: dielectric constant (Wed Jun 29 2005 - 06:02:24 CDT)
  • Re: AMBER: SHAKE in md with partial solvation (Mon Jun 06 2005 - 05:34:09 CDT)
  • AMBER: pressure output (Thu Jun 02 2005 - 17:27:13 CDT)
  • Re: AMBER: size of solventbox (Wed Feb 23 2005 - 04:50:39 CST)
  • AMBER: clusters (Fri Feb 04 2005 - 06:36:48 CST)
  • RE: AMBER: non-periodic condition (Thu Feb 03 2005 - 14:42:34 CST)
  • Re: AMBER: units (Thu Jan 13 2005 - 05:33:16 CST)
  • Re: AMBER: units (Thu Jan 13 2005 - 05:35:07 CST)
  • Re: AMBER: Copper library? (Tue Jan 11 2005 - 04:40:55 CST)
  • Re: AMBER: .dat and frcmod files (Tue Jan 11 2005 - 04:46:03 CST)
  • AMBER: dynamics (Sat Jan 08 2005 - 13:51:30 CST)
• Gert Kiss
  • AMBER: Invalid Digit "*" (Wed Sep 28 2005 - 13:18:04 CDT)
  • AMBER: Build of AMBER for YDL ? (Wed Jun 01 2005 - 18:15:57 CDT)
• Giulio Rastelli
  • AMBER: INTRA molecular hbonds (Mon Jun 27 2005 - 09:09:23 CDT)
  • AMBER: adenine test for LMOD in amber8 (Thu Jun 16 2005 - 04:57:16 CDT)
  • AMBER: time and lifetime in hbond analysis (ptraj) (Tue Jun 14 2005 - 09:23:50 CDT)
  • AMBER: surfen and surfoff (Mon Mar 14 2005 - 10:21:22 CST)
  • AMBER: collision frequency in GBSA dynamics (Tue Jan 25 2005 - 12:33:33 CST)
• glc0358_at_vip.sina.com
  • RE: Re: AMBER: (Sat Jul 09 2005 - 05:37:54 CDT)
  • AMBER: (Sat Jul 09 2005 - 02:03:23 CDT)
  • AMBER: (Sat Jul 09 2005 - 01:22:45 CDT)
• Glen Otero
  • AMBER: Amber 8 and LAM compilation problem (Thu May 19 2005 - 00:52:00 CDT)
• Greg Recine
  • AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) (Thu Feb 17 2005 - 18:23:01 CST)
• Grzegorz Jezierski
  • AMBER: Incorrect imaging when using Periodic Boundary Conditions in NAMD with AMBER parameters (Thu Aug 04 2005 - 13:24:42 CDT)
  • Re: AMBER: Periodic box imaging using ptraj (Wed Jul 27 2005 - 06:28:29 CDT)
  • Re: AMBER: Periodic box imaging using ptraj (Wed Jul 27 2005 - 04:27:24 CDT)
  • AMBER: Thermodynamic Integration for conformational changes? (Tue Jul 26 2005 - 12:33:00 CDT)
  • AMBER: Periodic box imaging using ptraj (Tue Jul 26 2005 - 08:25:53 CDT)
  • AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" (Tue May 31 2005 - 11:04:20 CDT)
  • Re: AMBER: Unexpected stop of Sander run (Mon May 23 2005 - 09:38:58 CDT)
  • Re: AMBER: Unexpected stop of Sander run (Mon May 23 2005 - 08:43:51 CDT)
  • Re: AMBER: Unexpected stop of Sander run (Mon May 23 2005 - 02:14:54 CDT)
  • AMBER: Unexpected stop of Sander run (Sun May 22 2005 - 14:44:55 CDT)
  • AMBER: RESP charge fitting for N-methylguanine cation (Thu May 12 2005 - 11:50:17 CDT)
• gsciaini
  • Re: AMBER: How to modify force constants and equalibrium values for standard residues (Fri Jun 17 2005 - 08:41:44 CDT)
  • AMBER: non-periodic condition (Thu Feb 03 2005 - 10:40:46 CST)
• gsmith_at_ibab.ac.in
  • AMBER: parallel run (Tue Jan 11 2005 - 04:27:20 CST)
  • AMBER: istart2 (Mon Jan 10 2005 - 07:14:15 CST)
  • AMBER: error in parallel (Mon Jan 10 2005 - 02:18:51 CST)
• gtg549i_at_mail.gatech.edu
  • Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? (Tue Nov 22 2005 - 15:28:36 CST)
  • Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? (Tue Nov 22 2005 - 09:13:49 CST)
  • AMBER: how to extract the residues of first solvation shell from the simulated system after the production? (Mon Nov 21 2005 - 17:46:04 CST)
  • AMBER: Question about using MM_PBSA (Thu Nov 17 2005 - 15:28:19 CST)
  • AMBER: Build an acetone Box (Wed Sep 21 2005 - 02:18:49 CDT)
  • Re: AMBER: Make Distance restraints for non-standard residues (Fri Jun 10 2005 - 15:45:00 CDT)
  • AMBER: Make Distance restraints for non-standard residues (Fri Jun 10 2005 - 10:47:41 CDT)
  • AMBER: transfer data from Linux to windows (Thu Jun 09 2005 - 17:24:05 CDT)
  • Re: AMBER: question about loadiing pdb file of a molecule complex (Tue May 31 2005 - 14:12:39 CDT)
  • AMBER: Loading pdb-residue (re)numbering in leap (Tue May 31 2005 - 12:48:13 CDT)
  • Re: AMBER: question about loadiing pdb file of a molecule complex (Mon May 30 2005 - 10:56:09 CDT)
  • AMBER: question about loadiing pdb file of a molecule complex (Fri May 27 2005 - 16:39:28 CDT)
• Guanglei Cui
  • Re: AMBER: iwork array for nmr (Mon Nov 14 2005 - 17:17:31 CST)
  • Re: AMBER: About WHAM program (Wed Nov 02 2005 - 07:47:01 CST)
  • Re: AMBER: REMD error!!! (Thu Oct 20 2005 - 10:51:21 CDT)
  • Re: AMBER: QMMM question (Mon Oct 10 2005 - 09:14:20 CDT)
  • Re: AMBER: sander error (Mon Oct 10 2005 - 08:52:29 CDT)
  • Re: AMBER: REM error (Mon Sep 12 2005 - 20:04:33 CDT)
  • Re: AMBER: umbrella sampling output question (Mon Sep 12 2005 - 08:06:31 CDT)
  • Re: AMBER: broblem of replica exchange MD with polarizable force field (Thu Sep 01 2005 - 10:01:46 CDT)
  • AMBER: wtmol and resp (Mon Aug 15 2005 - 09:59:42 CDT)
  • Re: AMBER: Failed sander runs for large systems (Fri Jul 29 2005 - 23:33:27 CDT)
  • Re: AMBER: Error in MD (Thu Jul 21 2005 - 23:08:56 CDT)
  • Re: AMBER: atom type for -CH=CH- (Fri Jun 10 2005 - 08:56:52 CDT)
  • Re: AMBER: radius parameter for Mg2+ in mm_pbsa calculation (Sat Jun 04 2005 - 10:17:11 CDT)
  • Re: AMBER: Error on restrained MD equilibration (AMBER 7) (Wed Jun 01 2005 - 09:18:37 CDT)
  • Re: AMBER: Error on restrained MD equilibration (AMBER 7) (Tue May 31 2005 - 14:02:46 CDT)
  • Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? (Wed May 25 2005 - 08:55:23 CDT)
  • Re: AMBER: How to fix certain bond angles (Tue May 24 2005 - 10:40:00 CDT)
  • Re: AMBER: the restarting error (Mon Apr 25 2005 - 09:37:50 CDT)
  • Re: AMBER: intramolecular nonbonded interactions in AMBER force field (Fri Apr 22 2005 - 08:52:53 CDT)
  • Re: AMBER: Rep Exch. suggestion (Mon Apr 18 2005 - 08:37:37 CDT)
  • Re: AMBER: SollvateBox with ethanol (Fri Apr 15 2005 - 12:50:20 CDT)
  • Re: AMBER: leap single precision (Fri Apr 08 2005 - 11:19:38 CDT)
  • AMBER: leap single precision (Thu Apr 07 2005 - 13:04:20 CDT)
  • Re: AMBER: REM mdinfo file (Tue Mar 29 2005 - 12:00:10 CST)
  • Re: AMBER: antechamber availability (Wed Mar 23 2005 - 17:21:23 CST)
  • Re: AMBER: layer (Fri Mar 18 2005 - 09:13:32 CST)
  • Re: AMBER: Velocity Info (Wed Mar 16 2005 - 10:29:35 CST)
  • Re: AMBER: Velocity Info (Wed Mar 16 2005 - 08:55:07 CST)
  • Re: AMBER: gyration radius (Sun Mar 13 2005 - 12:18:18 CST)
  • Re: AMBER: mesure dihedral angle during MD (Sun Mar 13 2005 - 12:10:46 CST)
  • Re: AMBER: Controlling number of water residues... (Tue Mar 01 2005 - 09:49:57 CST)
  • Re: AMBER: ico(i)=-1? (Sat Feb 26 2005 - 09:42:08 CST)
  • Re: FW: AMBER: mpirun sander8 problem (Thu Feb 24 2005 - 09:46:05 CST)
  • Re: AMBER: change of prmtop file (Wed Feb 02 2005 - 12:03:53 CST)
  • Re: AMBER: skip snapshots with ptraj in amber 8.0 (Mon Jan 31 2005 - 16:19:27 CST)
  • AMBER: system size limit (Sun Jan 23 2005 - 23:54:06 CST)
  • Re: AMBER: Sander Replica Exchange exits with unit 6 error (Mon Jan 17 2005 - 13:31:07 CST)
  • Re: AMBER: Sander Replica Exchange exits with unit 6 error (Mon Jan 17 2005 - 10:09:03 CST)
  • Re: AMBER: Problem with restart file (Thu Jan 13 2005 - 09:40:14 CST)
• Guangyu Sun
  • Re: AMBER: No. of Snapshots in MM/GB/SA (Tue Apr 12 2005 - 13:17:35 CDT)
• GUILBAUD Philippe 153683
  • AMBER: Polarization & energy analysis (Fri Nov 18 2005 - 04:52:26 CST)
• Guillaume Bollot
  • AMBER: GBSA simulation problem (Mon Oct 31 2005 - 02:23:26 CST)
  • AMBER: AMBER 8 : Water cap problem (Mon Feb 14 2005 - 07:14:20 CST)
  • AMBER: AMBER 8: Freeze AND restrain questions (Mon Jan 24 2005 - 10:19:11 CST)
• Guillermo Mulliert Carlín
  • AMBER: AMBER 8.0 problems with impose (tleap) on linux (Tue Apr 05 2005 - 01:35:17 CDT)
• Gustavo Pierdominici Sottile
  • AMBER: vdw of h atoms (Fri Oct 28 2005 - 14:16:10 CDT)
  • AMBER: shake (Fri Aug 19 2005 - 11:37:46 CDT)
  • AMBER: min problem (Tue Aug 16 2005 - 18:05:56 CDT)
  • AMBER: bond parameters (Wed Aug 03 2005 - 09:39:34 CDT)
  • AMBER: sp2 carbon atom parametrization (Tue Jun 14 2005 - 11:30:16 CDT)
  • AMBER: checkoverlap (Thu Jun 02 2005 - 12:45:19 CDT)
  • AMBER: layer (Fri Mar 18 2005 - 08:42:53 CST)
  • AMBER: vlimit (Fri Mar 11 2005 - 06:33:36 CST)
  • AMBER: vlimit heat (Wed Mar 09 2005 - 11:36:30 CST)
  • AMBER: vlimit in heating (Wed Mar 09 2005 - 08:13:20 CST)
  • AMBER: heating (Tue Mar 08 2005 - 16:20:34 CST)
  • AMBER: vlimit (Fri Feb 25 2005 - 06:45:35 CST)
  • AMBER: correlation (Thu Feb 24 2005 - 13:48:50 CST)
  • AMBER: classes (Wed Feb 23 2005 - 15:00:47 CST)
  • AMBER: ptraj (Fri Feb 18 2005 - 08:58:37 CST)
  • AMBER: rms (Wed Feb 16 2005 - 07:14:50 CST)
  • AMBER: (Wed Feb 16 2005 - 06:22:59 CST)
  • AMBER: check in leap (Tue Feb 15 2005 - 13:34:21 CST)
  • AMBER: blows up (Tue Feb 15 2005 - 13:11:43 CST)
  • AMBER: constrains (Mon Feb 14 2005 - 08:53:18 CST)
  • AMBER: vlimit (Mon Feb 14 2005 - 06:23:31 CST)
  • AMBER: archive (Fri Feb 11 2005 - 08:58:33 CST)
  • AMBER: ptraj error and min problems (Fri Feb 11 2005 - 08:54:23 CST)
  • AMBER: minimization.out (Wed Feb 09 2005 - 13:32:01 CST)
  • AMBER: energy plot in minimization (Wed Feb 09 2005 - 11:36:25 CST)
  • AMBER: problem in minimization (Tue Feb 08 2005 - 12:31:17 CST)
  • AMBER: problem in writing (Mon Feb 07 2005 - 13:59:49 CST)
  • AMBER: change of prmtop file (Wed Feb 02 2005 - 09:43:34 CST)
  • AMBER: doubts with a new aminoacid (Tue Feb 01 2005 - 14:28:52 CST)
  • AMBER: details of new aminoacid (Tue Jan 18 2005 - 07:01:15 CST)
  • AMBER: new aminoacid (Mon Jan 17 2005 - 10:26:32 CST)
  • AMBER: protonate (Fri Jan 14 2005 - 12:05:49 CST)
• haixiao jin
  • AMBER: the averaged structure VS the specific snapshot (Thu Dec 22 2005 - 22:24:04 CST)
  • AMBER: does the result of H bond is consistent with the ∆Eele of MM_PBSA? (Thu Dec 22 2005 - 22:12:46 CST)
  • Re: AMBER: MM_PBSA problem (Mon Nov 07 2005 - 02:59:27 CST)
  • Re: AMBER: MM_PBSA problem (Fri Nov 04 2005 - 02:58:14 CST)
  • AMBER: MM_PBSA problem (Fri Nov 04 2005 - 00:43:49 CST)
  • AMBER: with two water molecules in active site, how to calculate the free energy of ligand bound to complex? (Mon Oct 31 2005 - 00:27:08 CST)
  • AMBER: How to calculate binding free energy of ligand bound to complex with two active-site water molecules? (Tue Oct 25 2005 - 02:55:46 CDT)
  • Re: AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue (Thu Oct 20 2005 - 21:03:43 CDT)
  • Re: AMBER: ptraj hbond analysis (Thu Oct 20 2005 - 06:07:30 CDT)
  • AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue (Thu Oct 20 2005 - 05:49:29 CDT)
  • Re: AMBER: about the %occupied of hydrogen bond (Mon Sep 19 2005 - 10:17:31 CDT)
  • Re: AMBER: about the %occupied of hydrogen bond (Mon Sep 19 2005 - 09:12:42 CDT)
  • Re: AMBER: about the %occupied of hydrogen bond (Sun Sep 18 2005 - 23:44:07 CDT)
  • AMBER: about the %occupied of hydrogen bond (Wed Sep 14 2005 - 00:39:05 CDT)
  • AMBER: The “crystallographic” waters should be retained or deleted? (Wed Aug 10 2005 - 07:35:34 CDT)
  • Re: AMBER: RE: is calculated B-factors always smaller than experimental ones? (Tue Aug 09 2005 - 00:47:19 CDT)
  • Re: AMBER: is calculated B-factors always smaller than experimental ones? (Mon Aug 08 2005 - 00:33:48 CDT)
  • AMBER: How to calculate hydrogen bond involved with water molecules quickly? (Mon Aug 08 2005 - 00:07:48 CDT)
  • AMBER: is calculated B-factors always smaller than experimental ones? (Sun Aug 07 2005 - 09:57:54 CDT)
  • AMBER: how the phosphated threonine to be recognized in leap (Thu Jun 23 2005 - 04:03:26 CDT)
  • AMBER: no corrected reaction field energy in *.out files after running mm_pbsa (Sun Jun 12 2005 - 21:04:40 CDT)
• Hannes Barsch
  • AMBER: AMBER tests (x86-64, PGI / Intel) (Wed Oct 26 2005 - 02:54:36 CDT)
  • AW: AMBER: compiling amber with pgi 5.2.4 (Tue Oct 25 2005 - 10:42:53 CDT)
  • AMBER: compiling amber with pgi 5.2.4 (Mon Oct 24 2005 - 07:21:11 CDT)
  • AMBER: conformational sampling of a peptide (Tue May 24 2005 - 03:58:04 CDT)
  • AMBER: leap problem: savepdb (Fri May 20 2005 - 04:30:29 CDT)
  • AMBER: peptide side chain modification with LEAP (Tue Apr 12 2005 - 09:19:53 CDT)
• Hannes Loeffler
  • AMBER: How to check for water mediated hydrogen bonds? (Sun Nov 27 2005 - 22:52:44 CST)
  • AMBER: program to visualize crystal symmetries (Tue Oct 18 2005 - 03:36:31 CDT)
• Harianto
  • Re: AMBER: ambpdb radii (Fri Feb 25 2005 - 12:41:59 CST)
  • Re: AMBER: ambpdb radii (Fri Feb 25 2005 - 10:20:31 CST)
  • AMBER: ambpdb radii (Thu Feb 24 2005 - 13:24:39 CST)
  • Re: AMBER: Increasing Volume with ntb=1 (Thu Jan 27 2005 - 11:49:52 CST)
  • Re: AMBER: Increasing Volume with ntb=1 (Wed Jan 26 2005 - 17:19:59 CST)
  • AMBER: Increasing Volume with ntb=1 (Wed Jan 26 2005 - 14:12:29 CST)
  • AMBER: Cutoff for anal (Thu Jan 20 2005 - 11:50:14 CST)
• Harianto Tjong
  • AMBER: pH=1 MD simulation (Tue Nov 15 2005 - 16:16:12 CST)
  • Re: AMBER: restart file (Tue Jul 05 2005 - 15:49:16 CDT)
  • AMBER: restart file (Tue Jul 05 2005 - 13:49:20 CDT)
  • Re: AMBER: rborn(i) in egb.f (Tue May 03 2005 - 17:13:16 CDT)
  • Re: AMBER: rborn(i) in egb.f (Tue May 03 2005 - 15:31:43 CDT)
  • AMBER: rborn(i) in egb.f (Tue May 03 2005 - 14:04:39 CDT)
• hayden
  • AMBER: gaff sugar residue instability (Thu Nov 24 2005 - 08:43:03 CST)
  • AMBER: RE: gaff sugar residue instability (Tue Nov 22 2005 - 13:32:14 CST)
  • AMBER: unstable MD velocities (Thu Sep 01 2005 - 12:38:11 CDT)
• Hayden Eastwood
  • AMBER: creating residues - charge assign problems (Fri May 13 2005 - 06:06:06 CDT)
  • AMBER: Replica Exchange crashing (Fri Mar 18 2005 - 06:39:48 CST)
• heddi
  • AMBER: LEAP (Tue Jan 25 2005 - 07:42:36 CST)
• Heike.Meiselbach_at_chemie.uni-erlangen.de
  • Re: AMBER: problem with xleap (Tue Oct 18 2005 - 09:07:02 CDT)
• Heiko Meyer
  • Re: AMBER: restart file and crd file (Fri Nov 04 2005 - 09:49:18 CST)
  • Re: AMBER: restart file and crd file (Fri Nov 04 2005 - 06:56:41 CST)
  • Re: AMBER: capping? (Wed Mar 09 2005 - 11:17:01 CST)
  • AMBER: solvatebox problem in the antechamber tutorial (Wed Mar 09 2005 - 10:29:00 CST)
• Herbert Georg
  • Re: AMBER: Question about GAFF atom types (Mon Jun 20 2005 - 11:47:38 CDT)
  • Re: AMBER: Question about GAFF atom types (Fri Jun 17 2005 - 17:31:52 CDT)
  • Re: AMBER: Question about GAFF atom types (Fri Jun 17 2005 - 14:49:53 CDT)
  • AMBER: Question about GAFF atom types (Thu Jun 16 2005 - 14:18:50 CDT)
• hj zou
  • Re: Re: AMBER: how to reduce box size and delete excess solvent (Wed Jul 27 2005 - 08:36:40 CDT)
  • AMBER: antechamber problems (Sun Jun 19 2005 - 08:50:08 CDT)
  • AMBER: antechamber problems (Fri Jun 17 2005 - 08:32:27 CDT)
  • AMBER: how to reduce box size and delete excess solvent (Sun May 15 2005 - 06:51:32 CDT)
  • AMBER: how can I deal with the puzzle? (Tue Mar 08 2005 - 21:36:39 CST)
  • AMBER: What PRESS is? (Mon Mar 07 2005 - 21:08:39 CST)
• HL Eastwood
  • AMBER: re: leap compilation problems xeon EM64 processor (Mon Dec 19 2005 - 09:30:57 CST)
  • AMBER: compiling leap with Xeon EM64 (suse linux 9.2) (Mon Dec 19 2005 - 09:17:08 CST)
  • AMBER: generate charmm paramater file from amber parm file (Wed Feb 16 2005 - 11:19:56 CST)
• Holger Gohlke
  • Re: AMBER: MM-PBSA: plot the "Ggas+Gsol" vs time (Thu Dec 01 2005 - 01:06:49 CST)
  • Re: AMBER: Can GB and MS work correctly together in mmpbsa? (Fri Jul 15 2005 - 00:39:21 CDT)
  • Re: AMBER: nmode in mmpbsa (Tue May 17 2005 - 01:44:17 CDT)
  • Re: AMBER: MM_PBSA error (Tue Apr 12 2005 - 01:30:24 CDT)
  • Re: AMBER: MM_PBSA error (Mon Apr 11 2005 - 15:49:37 CDT)
  • Re: AMBER: ptraj analysis (Thu Jan 20 2005 - 01:28:27 CST)
  • Re: AMBER: RMS fluctuations along modes obtained from PCA (Wed Jan 19 2005 - 08:51:10 CST)
  • Re: AMBER: PBCAL=0. Problems in MM/PBSA (Fri Jan 14 2005 - 01:31:45 CST)
• Holly Freedman
  • AMBER: vlimit exceeded in thermalization (Mon Mar 28 2005 - 22:16:12 CST)
  • AMBER: total energy of solvation (Tue Feb 22 2005 - 22:05:36 CST)
• hornak_at_csb.sunysb.edu
  • Re: AMBER: atommask error (Fri Apr 29 2005 - 02:41:09 CDT)
• Huaer XC
  • AMBER: mixture solvent model (Wed Apr 27 2005 - 23:13:11 CDT)
  • AMBER: Solvate with mixture of ethanol and water(Newbie question) (Wed Apr 27 2005 - 00:41:00 CDT)
  • AMBER: SollvateBox with ethanol (Fri Apr 15 2005 - 11:21:01 CDT)
• huhu
  • AMBER: TI tutorial in Amber 8 (Wed Jun 08 2005 - 04:52:24 CDT)
• Hui-Hsu Tsai
  • AMBER: NOE constraints (Tue May 03 2005 - 14:18:27 CDT)
  • Re: AMBER: "personality" of Amber force field (Fri Mar 18 2005 - 17:05:07 CST)
  • Re:AMBER: "personality" of Amber force field (Fri Mar 18 2005 - 15:22:11 CST)
  • AMBER: "personality" of Amber force field (Wed Mar 16 2005 - 10:01:00 CST)
  • Re: AMBER: spherical boundary condition (Mon Mar 14 2005 - 12:59:01 CST)
  • AMBER: spherical boundary condition (Sat Mar 12 2005 - 13:05:52 CST)
  • AMBER: capping? (Tue Mar 08 2005 - 15:34:59 CST)
• HuiZhe Li
  • AMBER: compile amber8 on RHEL4 (Fri Feb 25 2005 - 01:59:02 CST)
• Husni Fattayer
  • Re: AMBER: how to pull out frames (Mon Jun 13 2005 - 06:22:40 CDT)
  • Re: AMBER: mm_pbsa problem (Wed Apr 27 2005 - 10:09:40 CDT)
  • AMBER: mm_pbsa problem (Mon Apr 25 2005 - 15:59:22 CDT)
• Hwankyu Lee
  • AMBER: Convert .prmtop (AMBER7/8) to old format (AMBER6) (Fri Aug 05 2005 - 22:44:07 CDT)
  • AMBER: temperature keep increasing in high temp. (Fri Jul 29 2005 - 16:27:04 CDT)
  • Re: AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 18:48:56 CDT)
  • Re: AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 18:26:16 CDT)
  • Re: AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 17:47:29 CDT)
  • AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 08:55:57 CDT)
  • AMBER: eigenvalues in vector of ptraj (Wed Jun 01 2005 - 07:53:51 CDT)
  • Re: AMBER: density profiles in ptraj or carnal (Mon May 30 2005 - 23:13:26 CDT)
  • Re: AMBER: density profiles in ptraj or carnal (Mon May 30 2005 - 17:58:54 CDT)
  • AMBER: density profiles in ptraj or carnal (Sun May 29 2005 - 22:27:37 CDT)
  • Re: AMBER: Error: vlimit exceeded for step (Tue May 24 2005 - 13:34:34 CDT)
  • Re: AMBER: Error: vlimit exceeded for step (Tue May 24 2005 - 13:07:41 CDT)
  • AMBER: Error: vlimit exceeded for step (Tue May 24 2005 - 12:20:10 CDT)
  • Re: AMBER: Connecting two molecules (Mon May 23 2005 - 11:51:20 CDT)
  • AMBER: Connecting two molecules (Mon May 23 2005 - 10:13:00 CDT)
  • AMBER: Error in sander: stack trace terminated abnormally. (Sun May 22 2005 - 16:05:31 CDT)
  • Re: AMBER: rotating and repositioning molecules in xleap (Sun May 22 2005 - 08:03:40 CDT)
  • AMBER: rotating and repositioning molecules in xleap (Sat May 21 2005 - 01:09:45 CDT)
  • AMBER: generating over 16 bps of DNA in nucgen (Mon May 16 2005 - 10:33:04 CDT)
  • AMBER: Calculating of radius of gyration in Carnal (Sat May 14 2005 - 13:36:37 CDT)
  • Re: AMBER: doesn't work in pmemd, and no output in parallel simulations (Tue Apr 26 2005 - 21:46:09 CDT)
  • AMBER: doesn't work in pmemd, and no output in parallel simulations (Tue Apr 26 2005 - 15:35:26 CDT)
  • Re: AMBER: A question on connecting residues in xleap (Mon Apr 11 2005 - 09:49:47 CDT)
  • Re: AMBER: A question on connecting residues in xleap (Sun Apr 10 2005 - 16:22:16 CDT)
  • AMBER: A question on connecting residues in xleap (Sun Apr 10 2005 - 11:54:55 CDT)
  • AMBER: Making prepin file for individual residues of huge molecule. (Mon Mar 21 2005 - 09:00:11 CST)
  • Re: AMBER: Making topology files of big moleucles in antechamber (Fri Mar 18 2005 - 10:48:02 CST)
  • AMBER: Making topology files of big moleucles in antechamber (Thu Mar 17 2005 - 10:09:06 CST)
• Ian Withers
  • Re: AMBER: Topology Format Amber 8 (Tue Feb 15 2005 - 07:33:15 CST)
• Ilan Samish
  • Re: AMBER: molecular dynamics course (Sun Jul 10 2005 - 01:23:05 CDT)
• ilaria massarelli
  • RE: AMBER: NaNQ (Wed Mar 02 2005 - 09:01:33 CST)
  • AMBER: NaNQ (Tue Mar 01 2005 - 02:45:10 CST)
• Ilyas Yildirim
  • Re: AMBER: antechamber problem (Fri Dec 30 2005 - 18:25:38 CST)
  • Re: AMBER: Re: Ligand problem (Tue Dec 20 2005 - 18:39:02 CST)
  • Re: AMBER: regarding ambpdb (Thu Dec 01 2005 - 04:54:03 CST)
  • Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list (Tue Nov 15 2005 - 22:43:09 CST)
  • Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list (Thu Nov 10 2005 - 20:58:23 CST)
  • Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list (Wed Nov 09 2005 - 21:56:24 CST)
  • Re: AMBER: rounding in xleap when using saveoff command... (Wed Nov 02 2005 - 19:15:36 CST)
  • Re: AMBER: Leap error: Could not find atom type: CE (Wed Nov 02 2005 - 12:31:23 CST)
  • Re: AMBER: Improper Torsional Parameters (Wed Nov 02 2005 - 12:00:50 CST)
  • AMBER: rounding in xleap when using saveoff command... (Fri Oct 28 2005 - 20:26:22 CDT)
  • AMBER: Improper Torsional Parameters (Fri Oct 28 2005 - 19:59:35 CDT)
  • Re: AMBER: Solution for those who have mpich problem while building the parallel version of AMBER 8 (Wed Aug 17 2005 - 19:04:37 CDT)
  • AMBER: Solution for those who have mpich problem while building the parallel version of AMBER 8 (Tue Aug 16 2005 - 20:40:11 CDT)
  • Re: AMBER: Atom type problem (Thu Aug 11 2005 - 11:40:12 CDT)
  • Re: AMBER: Atom type problem (Thu Aug 11 2005 - 10:15:28 CDT)
  • RE: AMBER: Leap set head/tail question (Wed Aug 03 2005 - 16:40:23 CDT)
  • Re: AMBER: Fatal Error on loading a pdb in xLeap (Thu Jul 28 2005 - 22:56:32 CDT)
  • Re: AMBER: prepi format and question about it (Thu Jul 28 2005 - 00:10:36 CDT)
  • AMBER: prepi format and question about it (Wed Jul 27 2005 - 04:20:00 CDT)
  • Re: AMBER: SHAKE error (Fri Jul 22 2005 - 14:23:06 CDT)
  • Re: AMBER: TI - frcmod file (Wed Jul 13 2005 - 16:32:41 CDT)
  • Re: FW: AMBER: TI - frcmod file (Wed Jul 13 2005 - 15:51:00 CDT)
  • Re: AMBER: TI - frcmod file (Wed Jul 13 2005 - 15:42:49 CDT)
  • Re: AMBER: TI - frcmod file (Tue Jul 12 2005 - 17:06:53 CDT)
  • Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends (Mon Jul 11 2005 - 20:25:00 CDT)
  • Re: AMBER: tyrosyl charges (Thu Jul 07 2005 - 17:30:20 CDT)
  • Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends (Thu Jul 07 2005 - 16:56:14 CDT)
  • Re: AMBER: question about sander minimization error (Thu Jul 07 2005 - 03:59:13 CDT)
  • Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends (Wed Jul 06 2005 - 22:18:46 CDT)
  • Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends (Wed Jul 06 2005 - 17:24:45 CDT)
  • Re: AMBER: loading DNA-RNA hybrid in xleap (Sun Jul 03 2005 - 06:23:56 CDT)
  • Re: AMBER: TI-FEP for ALA --> GLY (Tue Jun 28 2005 - 00:46:17 CDT)
  • Re: AMBER: TI-FEP for VAL --> ALA (Mon Jun 27 2005 - 18:43:16 CDT)
  • Re: AMBER: TI-FEP for VAL --> ALA (Sat Jun 25 2005 - 18:39:11 CDT)
  • Re: AMBER: TI-FEP for ALA --> GLY (Sat Jun 25 2005 - 01:48:36 CDT)
  • Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends (Wed Jun 22 2005 - 17:13:19 CDT)
  • AMBER: RESP charges of RNA nucleotides with 3' and 5' ends (Mon Jun 20 2005 - 20:51:11 CDT)
  • Re: AMBER: Question about GAFF atom types (Mon Jun 20 2005 - 14:51:59 CDT)
  • Re: AMBER: Analysing my simulation data.. (Sat Jun 18 2005 - 11:47:06 CDT)
  • Re: AMBER: Question about GAFF atom types (Fri Jun 17 2005 - 20:29:24 CDT)
  • Re: AMBER: Question about GAFF atom types (Fri Jun 17 2005 - 15:42:18 CDT)
  • Re: AMBER: my frcmod file created using parmchk (Mon May 23 2005 - 23:03:42 CDT)
  • Re: AMBER: crashing xleap (Fri May 20 2005 - 16:47:09 CDT)
  • Re: AMBER: how to creat leaprc.gaff (Fri May 20 2005 - 04:48:14 CDT)
  • Re: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue (Thu May 19 2005 - 02:37:22 CDT)
  • Re: AMBER: Can we load prmtop and inpcrd files into xleap? (Wed May 18 2005 - 23:47:49 CDT)
  • Re: AMBER: Can we load prmtop and inpcrd files into xleap? (Wed May 18 2005 - 23:00:07 CDT)
  • AMBER: Can we load prmtop and inpcrd files into xleap? (Wed May 18 2005 - 21:16:35 CDT)
  • Re: AMBER: parameter for sulfur in thio-glucoside residue (Wed May 18 2005 - 21:11:34 CDT)
  • Re: AMBER: loading pdb (Wed May 18 2005 - 15:21:24 CDT)
  • AMBER: ATOM TYPE (Mon May 16 2005 - 21:10:48 CDT)
  • AMBER: *** Proper torsion parameters missing *** (Mon May 16 2005 - 19:19:04 CDT)
  • Re: AMBER: Problem with xleap (Thu May 12 2005 - 18:14:38 CDT)
  • AMBER: Problem with xleap (Wed May 11 2005 - 20:45:50 CDT)
  • Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth (Thu Apr 28 2005 - 19:00:11 CDT)
  • Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth (Thu Apr 28 2005 - 18:34:48 CDT)
  • Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth (Wed Apr 27 2005 - 23:34:32 CDT)
  • AMBER: A problem in TI approach - test case: meth2eth and eth2meth (Mon Apr 25 2005 - 20:47:19 CDT)
  • Re: AMBER: Free energy pertubation (thermodynamic intergration) (Mon Apr 25 2005 - 15:43:36 CDT)
  • Re: AMBER: About NAB (Thu Apr 14 2005 - 19:19:14 CDT)
  • AMBER: About NAB (Wed Apr 13 2005 - 19:19:32 CDT)
  • AMBER: nscm (Tue Apr 12 2005 - 09:55:50 CDT)
  • Re: AMBER: "The system has extended beyond" error (Thu Mar 31 2005 - 06:26:21 CST)
  • AMBER: "The system has extended beyond" error (Tue Mar 29 2005 - 16:28:35 CST)
  • Re: AMBER: periodicity problem (Wed Mar 16 2005 - 15:25:39 CST)
  • AMBER: Compiling just sander (Thu Mar 10 2005 - 21:07:31 CST)
  • Re: AMBER: heating (Tue Mar 08 2005 - 17:02:17 CST)
  • Re: AMBER: Dummy atoms: Changing the source code (Tue Mar 08 2005 - 14:56:48 CST)
  • Re: AMBER: Dummy atoms: Changing the source code (Fri Mar 04 2005 - 20:56:34 CST)
  • AMBER: Dummy atoms: Changing the source code (Thu Mar 03 2005 - 18:24:03 CST)
  • Re: AMBER: bond connectivity among dummy atoms (Thu Mar 03 2005 - 15:58:38 CST)
  • Re: AMBER: bond connectivity among dummy atoms (Thu Mar 03 2005 - 13:57:48 CST)
  • AMBER: vlimit problem (Fri Feb 25 2005 - 19:45:03 CST)
  • Re: AMBER: Antechamber/formatting question (Fri Feb 25 2005 - 19:31:46 CST)
  • Re: AMBER: lastrst (Tue Feb 22 2005 - 20:36:00 CST)
  • AMBER: Dummy Atom Types on both states (Mon Feb 14 2005 - 20:29:03 CST)
  • AMBER: nucgen problem (Fri Feb 11 2005 - 18:56:41 CST)
  • Re: AMBER: Creating an input file for GRASP using AMBER 8 (Mon Feb 07 2005 - 16:24:24 CST)
  • AMBER: Creating an input file for GRASP using AMBER 8 (Mon Feb 07 2005 - 13:07:29 CST)
  • Re: AMBER: new tutorial available (Wed Jan 26 2005 - 05:59:16 CST)
  • Re: AMBER: calculating electrostatic potential (Tue Jan 25 2005 - 12:26:32 CST)
  • AMBER: .dat and frcmod files (Mon Jan 10 2005 - 16:10:36 CST)
  • Re: AMBER: Dummy Atoms: How to create them? (Wed Jan 05 2005 - 15:05:22 CST)
  • Re: AMBER: Dummy Atoms: How to create them? (Tue Jan 04 2005 - 21:25:24 CST)
• Imran Khan
  • AMBER: Increase the runtime of Amber benchmarks (Wed Oct 26 2005 - 04:23:10 CDT)
  • Re: AMBER: AMBER goes in a Loop (Fri Oct 14 2005 - 11:37:44 CDT)
  • AMBER: AMBER goes in a Loop (Thu Oct 13 2005 - 12:05:40 CDT)
• ioana_at_pegasus.arc.nasa.gov
  • AMBER: residence time of electrons/holes in DNA (Wed Aug 17 2005 - 16:48:43 CDT)
• Ismael Childers
  • You wont believe these pr1ces on name-brannd soft's! kerchief (Wed May 11 2005 - 10:06:11 CDT)
• Istvan Kolossvary
  • AMBER: atommask question (Fri Sep 23 2005 - 10:57:44 CDT)
  • AMBER: Apologies - LMOD website down (Thu Jul 14 2005 - 09:39:54 CDT)
  • Re: AMBER: adenine test for LMOD in amber8 (Thu Jun 16 2005 - 08:16:22 CDT)
  • AMBER: Announcing the LMOD website (Mon Jun 13 2005 - 13:18:52 CDT)
• ivan_at_mmb.pcb.ub.es
  • Re: AMBER: reading frcmod torsional parameters (Tue Dec 13 2005 - 09:42:37 CST)
  • AMBER: reading frcmod torsional parameters (Mon Dec 12 2005 - 07:44:36 CST)
  • AMBER: How does leap choose params ? (Wed Sep 14 2005 - 09:47:14 CDT)
  • Re: AMBER: bond parameters (Wed Aug 03 2005 - 09:54:29 CDT)
  • Re: AMBER: An atom name with 4 characters is not compatible with Leap ? (Fri Jul 22 2005 - 03:16:52 CDT)
  • Re: AMBER: DNA strands separate (Wed Jul 06 2005 - 09:39:04 CDT)
  • Re: AMBER: DNA strands separate (Wed Jul 06 2005 - 08:40:18 CDT)
  • AMBER: DNA strands separate (Wed Jul 06 2005 - 05:39:24 CDT)
  • Re: AMBER: Stacking energy (Fri Jul 01 2005 - 03:44:57 CDT)
  • AMBER: Gibbs perturb DNA strands separate (Tue Jun 07 2005 - 06:16:41 CDT)
• Jack Lei
  • Re: AMBER: coordinates translation (Sun Apr 24 2005 - 18:51:16 CDT)
  • Re: AMBER: Sander: idecomp (Tue Mar 15 2005 - 17:57:21 CST)
• Jagdish Rai
  • AMBER: D-amino acid prep-files(simple method) (Sun Jan 23 2005 - 08:18:45 CST)
  • AMBER: SO4 prep file (Tue Jan 18 2005 - 06:36:42 CST)
• Jakub Kostal
  • AMBER: using constraints with QM/MM (Wed Oct 26 2005 - 13:58:40 CDT)
• James Link
  • EBAY Update Information (Thu Sep 22 2005 - 12:55:50 CDT)
• James W. Caldwell
  • RE: AMBER: MPI for sander8 (Tue Feb 22 2005 - 13:52:56 CST)
• Jana Precechtelova
  • AMBER: hbond analysis in ptaj/carnal (Thu May 26 2005 - 11:25:20 CDT)
• Jaroslav Hanus
  • Re: AMBER: restraint only for Z cartegian coordinate? (Fri Feb 25 2005 - 05:12:48 CST)
  • AMBER: restraint only for Z cartegian coordinate? (Tue Feb 22 2005 - 09:40:58 CST)
• JAVIER PEREZ
  • AMBER: about resp (Wed Dec 07 2005 - 06:12:48 CST)
  • AMBER: center-of-mass distance restraints (Thu Jun 02 2005 - 06:14:15 CDT)
  • AMBER: distance restraints between two centers of mass (Thu May 26 2005 - 03:37:30 CDT)
• Javier Perez Miron
  • AMBER: ptraj for RDF calculations (Mon Feb 21 2005 - 02:42:33 CST)
  • AMBER: ptraj for RDF calculations (Sat Feb 19 2005 - 10:47:02 CST)
  • AMBER: IGB parameter (Wed Jan 19 2005 - 11:09:38 CST)
  • AMBER: PBCAL=0. Problems in MM/PBSA (Thu Jan 13 2005 - 14:41:29 CST)
• Javier Pérez Mirón
  • AMBER: maxgrp error (Tue Oct 11 2005 - 14:55:46 CDT)
• JIANING WANG
  • Re: AMBER: questions about MG ions (Mon Aug 01 2005 - 09:27:45 CDT)
  • AMBER: questions about MG ions (Sun Jul 31 2005 - 18:12:36 CDT)
• Jianzhong Liu
  • AMBER: Any way to get different charge on same type atom (Wed Nov 30 2005 - 17:07:28 CST)
  • Re: AMBER: Resp install problem, again (Wed Nov 16 2005 - 12:55:06 CST)
  • Re: AMBER: Resp install problem, again (Wed Nov 16 2005 - 12:14:51 CST)
  • AMBER: Resp install problem, again (Thu Nov 10 2005 - 10:03:24 CST)
  • AMBER: Resp install problem (Wed Nov 09 2005 - 17:21:09 CST)
• Jiapu.Zhang_at_csiro.au
  • AMBER: | ERROR: Could not read coords from *.rst (Sat Dec 17 2005 - 17:59:22 CST)
  • AMBER: | ERROR: Could not read coords from rst file (Thu Dec 15 2005 - 20:26:46 CST)
  • AMBER: How to use XLEAP to link one atom in a monomer to another atom in another monomer? (where both the 2 monomers are in a same pdb file) (Sun Nov 20 2005 - 19:35:57 CST)
  • AMBER: How to generate a RMSd-residue number graph using AMBER8 ptraj? (Thu Nov 03 2005 - 19:16:17 CST)
• Jinzhi Lei
  • Re: Re: AMBER: Fail to load the trajectory file. (Tue Apr 12 2005 - 15:54:52 CDT)
  • Re: Re: Re: AMBER: Fail to load the trajectory file. (Mon Apr 11 2005 - 20:53:50 CDT)
  • Re: Re: AMBER: Fail to load the trajectory file. (Mon Apr 11 2005 - 20:00:14 CDT)
  • AMBER: Fail to load the trajectory file. (Mon Apr 11 2005 - 19:36:34 CDT)
• Jiri Matousek
  • Re: AMBER: solvateoct mymolecule CHCL3BOX 10 PROBLEM!!! (Fri Apr 01 2005 - 01:37:39 CST)
• Jiri Sponer
  • Re: AMBER: About Salt concentration (Fri Dec 16 2005 - 19:05:13 CST)
  • AMBER: AMBER vs QM: base pairing and stacking (Wed Dec 07 2005 - 12:22:02 CST)
  • Re: AMBER: vdw of h atoms (Fri Oct 28 2005 - 15:00:19 CDT)
  • Re: AMBER: simulation with Mg2+ ions and counter ions (Sat Jul 09 2005 - 03:50:10 CDT)
  • Re: AMBER: Stacking energy (Fri Jul 01 2005 - 10:00:03 CDT)
  • Re: AMBER: Stacking energy (Fri Jul 01 2005 - 09:01:24 CDT)
  • Re: AMBER: Stacking energy (Fri Jul 01 2005 - 04:52:45 CDT)
  • Re: AMBER: carnal - water-mediated HBond (Sun Jan 23 2005 - 08:52:55 CST)
• Jiten
  • AMBER: Fw: The default of HIS in leaprc : HID or HIE ? (Tue Oct 04 2005 - 11:34:54 CDT)
  • AMBER: The default of HIS in leaprc : HID or HIE ? (Tue Oct 04 2005 - 11:21:52 CDT)
  • Re: AMBER: Re: TI tutorial (Wed Jun 29 2005 - 12:24:19 CDT)
  • Re: AMBER: Re: TI tutorial (Wed Jun 29 2005 - 11:22:04 CDT)
  • Re: AMBER: Re: TI tutorial (Tue Jun 28 2005 - 22:46:17 CDT)
  • Re: AMBER: Re: TI tutorial (Tue Jun 28 2005 - 11:36:59 CDT)
  • AMBER: Fw: TI tutorial --> ALA --> GLY TI calculation (Tue Jun 28 2005 - 10:02:42 CDT)
  • AMBER: Re: TI tutorial (Tue Jun 28 2005 - 09:17:39 CDT)
  • Re: AMBER: TI-FEP for ALA --> GLY (Mon Jun 27 2005 - 21:24:56 CDT)
  • Re: AMBER: TI-FEP for VAL --> ALA (Sun Jun 26 2005 - 21:11:03 CDT)
  • Re: AMBER: MM_PBSA ! (Sun Jun 26 2005 - 19:43:13 CDT)
  • Re: AMBER: TI-FEP for VAL --> ALA (Sat Jun 25 2005 - 11:13:44 CDT)
  • AMBER: TI-FEP for ALA --> GLY (Sat Jun 25 2005 - 00:07:03 CDT)
  • AMBER: amber8 in IBM-SP4 (Mon Jan 31 2005 - 21:32:28 CST)
  • AMBER: PBSA residual and pairwise decompostion (Tue Jan 25 2005 - 07:43:38 CST)
  • Re: AMBER: MM_PBSA fillratio error (Wed Jan 05 2005 - 00:54:35 CST)
  • AMBER: MM_PBSA fillratio error (Mon Jan 03 2005 - 03:36:30 CST)
• Joachim Reichelt
  • Re: AMBER: Simple 3D Molecule Visualization (Tue Oct 18 2005 - 11:45:42 CDT)
• Joe Nolan
  • AMBER: Amber8 compilation error (Thu Sep 08 2005 - 14:47:08 CDT)
  • AMBER: Sander bomb - atom out of bounds (Thu Apr 21 2005 - 12:46:01 CDT)
  • AMBER: Sander/Mpich2 error with mpd_singinit (Thu Apr 14 2005 - 15:00:09 CDT)
  • AMBER: Amber8 Parallel installation troubles (Tue Mar 22 2005 - 13:03:05 CST)
  • Re: AMBER: Sander questions on dual-processor Sun with MPICH (Thu Mar 10 2005 - 10:46:23 CST)
  • AMBER: Sander questions on dual-processor Sun with MPICH (Tue Mar 08 2005 - 14:37:50 CST)
  • AMBER: Xleap execution problems on Solaris (Tue Mar 01 2005 - 14:51:26 CST)
  • Re: AMBER: Amber8 Solaris installation failure (Tue Mar 01 2005 - 09:23:06 CST)
  • Re: AMBER: Amber8 Solaris installation failure (Mon Feb 28 2005 - 14:24:28 CST)
  • Re: AMBER: Amber8 Solaris installation failure (Tue Feb 22 2005 - 17:34:50 CST)
  • Re: AMBER: Amber8 Solaris installation failure (Tue Feb 22 2005 - 14:12:02 CST)
  • AMBER: Amber8 Solaris installation failure (Thu Feb 17 2005 - 14:27:12 CST)
  • AMBER: Amber8 installation test possible failures (Tue Feb 08 2005 - 13:55:39 CST)
  • AMBER: Amber8 installation problems on Sparc/Solaris9 (Tue Jan 18 2005 - 10:17:35 CST)
• John
  • AMBER: MM-PBSA-big energies (Sun Jul 03 2005 - 16:31:56 CDT)
  • RE: AMBER: solvent accessible surface area (Tue Apr 19 2005 - 07:22:04 CDT)
  • AMBER: solvent accessible surface area (Tue Apr 19 2005 - 05:45:40 CDT)
  • AMBER: surface area (Mon Apr 04 2005 - 05:35:58 CDT)
• John Bushnell
  • Re: AMBER: running shell scripts in tleap? (Mon Feb 14 2005 - 17:32:32 CST)
• John D. Chodera
  • AMBER: Unformatted restart file cannot be read by sander when PME in use (AMBER8) (Sun Sep 25 2005 - 20:08:37 CDT)
• John Mongan
  • Re: AMBER: more data points on the parmchk problem (Wed Nov 30 2005 - 15:01:35 CST)
  • Re: AMBER: essential dynamics (Wed Aug 24 2005 - 11:27:46 CDT)
  • Re: AMBER: Can constant pH be used for minimization? (Tue Jun 14 2005 - 19:03:38 CDT)
  • Re: AMBER: rborn(i) in egb.f (Tue May 03 2005 - 13:26:15 CDT)
  • Re: AMBER: capping (Wed Apr 27 2005 - 11:50:43 CDT)
• John O'Mahony
  • AMBER: Creating an Ester with Antechamber/Gaff (Thu Dec 01 2005 - 03:46:40 CST)
• John S Zintsmaster
  • Re: AMBER: Time Correlation Functions with Amber (Tue Nov 08 2005 - 11:57:26 CST)
  • AMBER: Time Correlation Functions with Amber (Tue Nov 08 2005 - 10:15:45 CST)
  • AMBER: calculating time correlation functions with ptraj (Mon Nov 07 2005 - 10:39:38 CST)
• John S. Zintsmaster
  • Re: AMBER: Time Correlation Functions with Amber (Tue Nov 08 2005 - 13:56:54 CST)
• John Silvio Vieceli
  • AMBER: intramolecular nonbonded interactions in AMBER force field (Wed Apr 20 2005 - 17:06:48 CDT)
• John Vieceli
  • AMBER: group-based cutoff (Wed Aug 10 2005 - 19:44:56 CDT)
  • AMBER: Zymeworks job posting (Mon Aug 08 2005 - 12:11:42 CDT)
• jojartb_at_pharm.u-szeged.hu
  • AMBER: charges (Fri Sep 16 2005 - 02:33:00 CDT)
  • AMBER: QM/MM (Wed Aug 17 2005 - 06:42:06 CDT)
• Jordi Rodrigo
  • AMBER: Sander Replica Exchange exits with unit 6 error (Tue Jan 25 2005 - 08:28:13 CST)
  • AMBER: Sander Replica Exchange exits with unit 6 error (Tue Jan 18 2005 - 08:46:27 CST)
  • AMBER: Sander Replica Exchange exits with unit 6 error (Mon Jan 17 2005 - 08:57:53 CST)
  • AMBER: Sander Replica Exchange exits with unit 6 error (Mon Jan 17 2005 - 07:25:14 CST)
  • AMBER: Sander Replica Exchange exits with unit 6 error (Mon Jan 17 2005 - 06:37:00 CST)
  • AMBER: Sander Replica Exchange exits with unit 6 error] (Mon Jan 17 2005 - 02:02:51 CST)
• Joseph Fernandez
  • Ptraj question -- Re: AMBER: carnal problem (Thu Sep 08 2005 - 12:04:14 CDT)
  • AMBER: Error with antechamber (Wed Aug 03 2005 - 14:45:29 CDT)
  • AMBER: nmode in mmpbsa (Mon May 16 2005 - 18:36:28 CDT)
  • AMBER: Identifying water molecules with ptraj (Sun May 01 2005 - 16:00:59 CDT)
  • AMBER: Multiple dihedral restraints (follow up) (Wed Feb 02 2005 - 12:11:01 CST)
  • AMBER: Multiple dihedral restraints (Tue Feb 01 2005 - 11:29:40 CST)
• Joseph Nachman
  • Re: AMBER: program to visualize crystal symmetries (Tue Oct 18 2005 - 11:21:22 CDT)
  • Re: AMBER: How to simulate a crystal structure? (Wed Oct 12 2005 - 11:57:56 CDT)
  • AMBER: Format of atom specifiication after FIND (Tue Aug 16 2005 - 14:02:55 CDT)
  • Re: AMBER: conformational sampling of a peptide (Tue May 24 2005 - 10:26:52 CDT)
• Joseph W.Toporowski
  • AMBER: ptraj, hbond problem (Tue Apr 12 2005 - 19:07:35 CDT)
  • AMBER: ptraj: determining solvent/ion densities (Thu Mar 17 2005 - 19:40:38 CST)
  • AMBER: determining solvent/ion densities (Mon Mar 14 2005 - 17:35:25 CST)
• jpragati_at_ibab.ac.in
  • AMBER: Problem during production!! (Tue Oct 04 2005 - 03:33:48 CDT)
  • AMBER: Error check COM velocity!! (Mon Oct 03 2005 - 06:58:01 CDT)
  • AMBER: Problem during Production (Sat Sep 24 2005 - 09:04:10 CDT)
  • AMBER: Query: Problem during Production (Thu Sep 22 2005 - 08:52:05 CDT)
• Juan Fernandez Carmona
  • AMBER: amber code (Tue May 24 2005 - 05:08:00 CDT)
• julien
  • AMBER: porblem in ptraj (Thu Oct 20 2005 - 04:19:47 CDT)
  • AMBER: clustering (Thu Sep 22 2005 - 07:10:00 CDT)
  • Re: AMBER: AMBER-process_mdout.perl (Mon Jul 18 2005 - 02:48:01 CDT)
  • AMBER: gyration radius (Sun Mar 13 2005 - 10:49:50 CST)
  • AMBER: mesure dihedral angle during MD (Sun Mar 13 2005 - 10:52:01 CST)
• Julien Michel
  • Re: AMBER: GBSA and thermodynamic ensemble (Mon Jun 13 2005 - 14:51:23 CDT)
  • Re: AMBER: Dummy atoms: Changing the source code (Fri Mar 04 2005 - 03:44:31 CST)
  • Re: AMBER: Dummy Atom Types on both states (Tue Feb 15 2005 - 10:10:34 CST)
  • Re: AMBER: new tutorial available (Wed Jan 26 2005 - 07:48:55 CST)
  • Re: AMBER: ANTECHAMBER & DIVCON (Wed Jan 26 2005 - 05:09:05 CST)
• JunJun Liu
  • Re: AMBER: Free energy calculation for protein-protein complex usingMM_PBSA (Sat Oct 22 2005 - 02:45:25 CDT)
  • Re: AMBER: Mg2+ radius in my_parse_delphi.siz (Tue Sep 27 2005 - 02:11:45 CDT)
  • AMBER: Mg2+ radius in my_parse_delphi.siz (Mon Sep 26 2005 - 22:30:14 CDT)
  • Re: AMBER: Can I get each corresponding sanpshots' delta delta energy term from mm_pbsa (Mon Sep 19 2005 - 21:51:32 CDT)
  • Re: AMBER: How is the origin of the grid defined?(PBSA question) (Tue Aug 23 2005 - 03:46:03 CDT)
  • AMBER: How is the origin of the grid defined?(PBSA question) (Sun Aug 14 2005 - 11:35:46 CDT)
  • Re: AMBER: mm_pbsa (Fri Jul 29 2005 - 21:22:20 CDT)
  • Re: AMBER: mm_pbsa (Fri Jul 29 2005 - 19:58:53 CDT)
  • AMBER: why not minimize snapshots before MM/PBSA calculations (Tue Jul 26 2005 - 10:02:00 CDT)
  • AMBER: molsurf error in MM/PBSA calculation (Tue Jul 12 2005 - 08:43:55 CDT)
  • AMBER: Temperature varible in MMPBSA script (Fri Jul 01 2005 - 08:59:05 CDT)
  • AMBER: How to read unformatted restart file in PTRAJ ? (Wed Jun 29 2005 - 01:20:57 CDT)
  • Re: AMBER: PBSA error: PB bomb in pd_aaradi (Wed Jun 22 2005 - 10:17:43 CDT)
  • Re: AMBER: Is the MD simulation normal (Tue May 31 2005 - 21:01:07 CDT)
  • Re: AMBER: (Fri May 20 2005 - 21:41:24 CDT)
  • Re: AMBER: Problem with xleap (Thu May 12 2005 - 02:19:24 CDT)
  • Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) (Thu May 05 2005 - 19:37:36 CDT)
• Junmei Wang
  • RE: AMBER: about antechamber(amber8) (Thu Dec 15 2005 - 09:54:40 CST)
  • RE: AMBER: ESP exceeds the MAXESP(20000), (Thu Nov 10 2005 - 09:37:05 CST)
  • RE: AMBER: antechamber dimesion size, again (Thu Oct 06 2005 - 14:29:04 CDT)
  • RE: AMBER: antechamber problem (Tue Sep 20 2005 - 18:05:36 CDT)
  • RE: AMBER: AMBER antechamber; dimenion size (Wed Sep 07 2005 - 11:02:24 CDT)
  • RE: AMBER: Antechamber error "Cannot successfully assign bond type for this molecule" (Fri Sep 02 2005 - 15:30:29 CDT)
  • RE: AMBER: antechamber problems (Mon Jun 20 2005 - 11:35:12 CDT)
  • RE: RE: AMBER: Antechamber RESP failed for large organic molecule (Wed Jun 01 2005 - 11:54:42 CDT)
  • RE: AMBER: Antechamber RESP failed for large organic molecule (Tue May 31 2005 - 09:37:35 CDT)
  • RE: AMBER: GAFF angle parameters (Tue May 17 2005 - 17:08:47 CDT)
  • RE: AMBER: ATTN REVISION (Wed Apr 20 2005 - 09:31:47 CDT)
  • RE: AMBER: antechamber for cyano group (Tue Apr 19 2005 - 11:28:59 CDT)
  • RE: AMBER: gaff atom types (Tue Apr 19 2005 - 11:18:44 CDT)
  • RE: AMBER: Re: Re: AMBER: ATTN REVISION (Tue Apr 19 2005 - 11:08:58 CDT)
  • RE: AMBER: frcmod.mod_phipsi.2 (Tue Mar 15 2005 - 14:22:29 CST)
  • RE: AMBER: Antechamber/Divcon assigned charges (Thu Mar 03 2005 - 23:20:38 CST)
  • RE: AMBER: Dihedral Energy calculation (Tue Mar 01 2005 - 12:57:49 CST)
  • RE: AMBER: gaussian output file (Tue Feb 01 2005 - 17:03:22 CST)
• junwang
  • Re: AMBER: Need help in charge fitting through RESP (Mon Jun 13 2005 - 12:51:41 CDT)
  • Re: RE: RE: AMBER: Antechamber RESP failed for large organic molecule (Wed Jun 01 2005 - 16:18:05 CDT)
  • AMBER: External Field in AMBER? (Tue May 31 2005 - 21:19:38 CDT)
  • Re: RE: AMBER: Antechamber RESP failed for large organic molecule (Tue May 31 2005 - 11:58:33 CDT)
  • AMBER: Antechamber RESP failed for large organic molecule (Sun May 29 2005 - 14:57:59 CDT)
• justin litchfield
  • Re: AMBER: D-enantiomers (Wed Sep 21 2005 - 02:50:36 CDT)
  • AMBER: ptraj efficiency (Wed Aug 24 2005 - 13:13:03 CDT)
  • Re: AMBER: AMBER on g5 10.4 w/g95 or gfortran (Tue Aug 16 2005 - 11:27:26 CDT)
  • Re: AMBER: Leap compilation issues (Mon Jul 11 2005 - 20:55:54 CDT)
  • Re: AMBER: Leap compilation issues (Mon Jul 11 2005 - 20:25:10 CDT)
  • Re: AMBER: Leap compilation issues (Mon Jul 11 2005 - 01:49:33 CDT)
  • AMBER: Leap compilation issues (Sun Jul 10 2005 - 20:41:50 CDT)
  • Re: AMBER: Position Restraints! (Sat Jul 09 2005 - 19:08:15 CDT)
  • AMBER: leap issues on a powerbook (Sun Jun 12 2005 - 18:21:02 CDT)
• Jyh-Shyong Ho
  • AMBER: parallel AMBER/pmemd installation problem on Opteron (Tue Feb 22 2005 - 23:08:22 CST)
• jz7_at_duke.edu
  • AMBER: Methionine with both C-ter and N-ter (Tue Mar 22 2005 - 16:17:18 CST)
  • AMBER: wierd behavior of addions (Tue Mar 22 2005 - 13:22:54 CST)
  • AMBER: question about periodicity of torsion parameter (Fri Mar 18 2005 - 16:08:50 CST)
  • AMBER: question about amber parameter file format etc. (Wed Mar 16 2005 - 11:37:29 CST)
• K. Yarem
  • AMBER: AMBER frcmod+off input vs. prep input (Tue Jun 07 2005 - 11:57:19 CDT)
• kanon gemini
  • AMBER: Restraints (Mon Aug 22 2005 - 05:58:25 CDT)
• Kara Di Giorgio
  • AMBER: RMSD Calculations (Mon Dec 05 2005 - 09:22:03 CST)
  • AMBER: Quantifying DNA perterbation (Tue Nov 15 2005 - 19:44:03 CST)
  • AMBER: Quick question about xLeap (Thu Sep 08 2005 - 09:31:59 CDT)
  • AMBER: Energy Comparisons (Wed Aug 17 2005 - 17:00:44 CDT)
  • Re: AMBER: leap question (Sat Aug 06 2005 - 22:02:45 CDT)
  • Re: AMBER: leap question (Fri Aug 05 2005 - 20:56:40 CDT)
  • AMBER: leap question (Fri Aug 05 2005 - 11:38:47 CDT)
  • AMBER: Boron and Amber (Tue Aug 02 2005 - 15:18:46 CDT)
  • AMBER: Leap set head/tail question (Tue Aug 02 2005 - 13:01:08 CDT)
  • Re: AMBER: questions about MG ions (Sun Jul 31 2005 - 23:55:46 CDT)
  • Re: AMBER: Adding residues to a DNA sequence (Fri Jul 29 2005 - 11:39:43 CDT)
  • AMBER: Fatal Error on loading a pdb in xLeap (Thu Jul 28 2005 - 10:10:45 CDT)
  • Re: AMBER: Adding residues to a DNA sequence (Mon Jul 25 2005 - 21:20:53 CDT)
  • AMBER: Adding residues to a DNA sequence (Sun Jul 24 2005 - 20:50:45 CDT)
  • AMBER: Carbonane (Thu Jul 21 2005 - 19:55:26 CDT)
  • Re: AMBER: Leap problem (Fri Jul 15 2005 - 08:59:47 CDT)
  • Re: AMBER: Leap problem (Thu Jul 14 2005 - 20:19:00 CDT)
  • AMBER: Leap problem (Thu Jul 14 2005 - 19:06:50 CDT)
  • AMBER: Leap question (Thu Jul 14 2005 - 10:10:12 CDT)
  • Re: AMBER: AMBER on Mac OS X (Wed Jul 06 2005 - 11:46:11 CDT)
  • Re: AMBER: RED question (Mon Jun 27 2005 - 00:13:13 CDT)
  • AMBER: RED question (Sat Jun 25 2005 - 17:44:23 CDT)
  • AMBER: Working with a nickel-organometallic compound (Tue May 31 2005 - 18:36:30 CDT)
  • Re: AMBER: Can we load prmtop and inpcrd files into xleap? (Wed May 18 2005 - 23:10:36 CDT)
  • Re: AMBER: Can we load prmtop and inpcrd files into xleap? (Wed May 18 2005 - 21:45:43 CDT)
  • AMBER: frcmod info for Nickel (Wed May 18 2005 - 14:04:44 CDT)
  • Re: AMBER: RESP charge fitting for N-methylguanine cation (Thu May 12 2005 - 21:40:17 CDT)
  • AMBER: Odd Antechamber Behavior (Fri Apr 29 2005 - 23:48:01 CDT)
  • Re: AMBER: Formatting a restraint file (Thu Apr 14 2005 - 11:25:18 CDT)
  • Re: AMBER: Formatting a restraint file (Thu Apr 14 2005 - 10:26:17 CDT)
  • Re: AMBER: Formatting a restraint file (Wed Apr 13 2005 - 19:31:25 CDT)
  • Re: AMBER: MM-PBSA in protein-Zn-ligand system (Tue Apr 12 2005 - 21:50:20 CDT)
  • AMBER: Protein With Structural Ions (Tue Apr 12 2005 - 12:47:52 CDT)
  • Re: AMBER: Protein with structural ions (Tue Apr 12 2005 - 11:59:40 CDT)
  • RE: AMBER: Protein with structural ions (Tue Apr 12 2005 - 10:51:32 CDT)
  • Re: AMBER: Protein with structural ions (Mon Apr 11 2005 - 10:40:45 CDT)
  • Re: AMBER: Protein with structural ions (Sun Apr 10 2005 - 23:47:29 CDT)
  • Re: AMBER: Protein with structural ions (Sun Apr 10 2005 - 22:05:08 CDT)
  • Re: AMBER: Protein with structural ions (Fri Apr 08 2005 - 13:55:41 CDT)
  • Re: AMBER: Protein with structural ions (Fri Apr 08 2005 - 11:30:26 CDT)
  • Re: AMBER: Protein with structural ions (Fri Apr 08 2005 - 00:29:26 CDT)
  • AMBER: question about placing a substrate in a protein pocket (Thu Mar 24 2005 - 22:33:26 CST)
  • Re: AMBER: Antechamber/formatting question (Sun Feb 27 2005 - 19:13:19 CST)
  • Re: AMBER: Antechamber/formatting question (Fri Feb 25 2005 - 20:02:40 CST)
  • Re: AMBER: Antechamber/formatting question (Fri Feb 25 2005 - 18:43:36 CST)
  • Re: AMBER: Formatting Questions (Tue Feb 22 2005 - 15:48:46 CST)
  • Re: AMBER: Formatting Questions (Mon Feb 21 2005 - 20:03:37 CST)
  • AMBER: Formatting Questions (Mon Feb 21 2005 - 13:09:44 CST)
  • Re: AMBER: Antechamber/formatting question (Fri Feb 18 2005 - 12:20:40 CST)
  • AMBER: Antechamber help needed (Thu Feb 17 2005 - 11:24:34 CST)
  • AMBER: DIVCON optimization (Wed Feb 09 2005 - 13:46:03 CST)
  • AMBER: Tutorial Request (Sun Feb 06 2005 - 11:01:15 CST)
  • AMBER: Antechamber/formatting question (Fri Feb 04 2005 - 17:05:18 CST)
  • Re: AMBER: Problems with xLEaP (Fri Jan 28 2005 - 18:48:52 CST)
  • Re: AMBER: Problems with xLEaP (Fri Jan 28 2005 - 18:18:44 CST)
  • Re: AMBER: Problems with xLEaP (Fri Jan 28 2005 - 18:14:02 CST)
  • AMBER: Problems with xLEaP (Fri Jan 28 2005 - 16:04:14 CST)
• Kara Wald
  • Re: AMBER: RMSD Calculations (Mon Dec 05 2005 - 10:39:44 CST)
  • AMBER: Formatting a restraint file (Wed Apr 13 2005 - 15:57:24 CDT)
  • AMBER: Protein with structural ions (Tue Apr 05 2005 - 16:29:46 CDT)
  • AMBER: Mainchain example needed (Mon Feb 14 2005 - 15:43:06 CST)
  • Re: AMBER: DIVCON optimization (Wed Feb 09 2005 - 17:30:07 CST)
  • AMBER: Can someone recommend a tutorial? (Thu Jan 20 2005 - 14:28:46 CST)
  • AMBER: AMBER tutorial ambpdb question (Mon Jan 10 2005 - 19:33:44 CST)
• Karol Miaskiewicz
  • Re: AMBER: problem with running AMBER with lam-mpi though PBS script (Wed Mar 09 2005 - 07:57:46 CST)
  • Re: AMBER: amber on sgi (Wed Mar 09 2005 - 07:37:31 CST)
• Karsten Suhre
  • Re: AMBER: Simple 3D Molecule Visualization (Tue Oct 18 2005 - 11:45:36 CDT)
  • Re: AMBER: program to visualize crystal symmetries (Tue Oct 18 2005 - 04:13:23 CDT)
• Karthikeyan Pasupathy
  • AMBER: Position Restraints! (Sat Jul 09 2005 - 12:24:51 CDT)
• Katagiri Daisuke
  • AMBER: About Gaussian Key Words (Wed Apr 06 2005 - 22:10:12 CDT)
• Kateryna Miroshnychenko
  • AMBER: problem with improper torsions in parmchk (Mon Dec 26 2005 - 10:55:54 CST)
  • AMBER: parallel AMBER on cluster (Thu Dec 15 2005 - 12:16:17 CST)
  • Re:AMBER: about resp (Wed Dec 07 2005 - 07:50:07 CST)
  • Re: AMBER: seg fault error in resp (Thu Oct 27 2005 - 09:14:24 CDT)
  • Re: AMBER: seg fault error in resp (Wed Oct 26 2005 - 10:26:37 CDT)
  • AMBER: seg fault error in resp (Wed Oct 26 2005 - 08:24:37 CDT)
  • Re: AMBER: leap segmentation fault-bugfix1 didn't work (Tue Sep 13 2005 - 03:06:45 CDT)
  • AMBER: leap segmentation fault-bugfix1 didn't work (Fri Sep 09 2005 - 08:28:43 CDT)
  • AMBER: generation of conformations for multi-conf. RESP fitting (Tue Sep 06 2005 - 09:29:40 CDT)
  • Re: AMBER: fit (Mon Jul 25 2005 - 05:11:11 CDT)
  • AMBER: segmentation fault in radial ptraj (Mon Jul 18 2005 - 11:55:08 CDT)
  • AMBER: units of mwcovar matrix befor conversion (Thu Jul 14 2005 - 03:18:28 CDT)
  • AMBER: Re:Re:single-stranded poly(rC) simulation (Tue Apr 05 2005 - 12:37:54 CDT)
  • AMBER: single-stranded poly(rC) simulation (Mon Apr 04 2005 - 08:49:39 CDT)
  • AMBER: helical parameters obtaining (Sat Apr 02 2005 - 05:08:17 CST)
  • AMBER: Are the constant pH simulations with explicit water possible? (Tue Mar 29 2005 - 07:54:14 CST)
• Kathleen Erickson
  • Re: AMBER: amber8 parallel sander (Mon Oct 03 2005 - 15:37:47 CDT)
  • Re: AMBER: amber8 parallel sander (Thu Sep 22 2005 - 11:44:39 CDT)
• keiodai_at_shohoku.ac.jp
  • AMBER: Re: Amber 8 dual-Xeon compile problem (Wed Mar 09 2005 - 22:14:33 CST)
• Kenley Barrett
  • AMBER: using periodic boundary conditions to create infinite double helix (Wed Nov 16 2005 - 11:32:39 CST)
  • Re: AMBER: xleap with modified residue (Thu Oct 20 2005 - 13:25:41 CDT)
  • Re: AMBER: creating a resp input file without Gaussian. (Mon Sep 19 2005 - 14:08:25 CDT)
  • AMBER: using SALTCON for human cell cytoplasm (Sun Sep 18 2005 - 11:45:42 CDT)
  • AMBER: position of protonation info from constant pH run (Wed Jun 15 2005 - 20:27:44 CDT)
  • AMBER: Can constant pH be used for minimization? (Fri Jun 10 2005 - 16:34:41 CDT)
  • Re: AMBER: segmentation fault in sander (Tue Jun 07 2005 - 10:36:44 CDT)
  • AMBER: segmentation fault in sander (Mon Jun 06 2005 - 17:07:59 CDT)
  • AMBER: error in chirality.c? (Wed May 25 2005 - 09:27:07 CDT)
  • Re: AMBER: crashing xleap (Fri May 20 2005 - 15:57:00 CDT)
  • AMBER: crashing xleap (Fri May 20 2005 - 13:48:13 CDT)
  • AMBER: a nomenclature question (Fri May 06 2005 - 11:11:24 CDT)
  • AMBER: Calculate vdw parameters for alkaline earth metal ions (Fri Apr 22 2005 - 17:19:23 CDT)
  • Re: AMBER: problems with "protonate" (Mon Apr 11 2005 - 16:20:47 CDT)
  • AMBER: problems with "protonate" (Thu Apr 07 2005 - 21:27:07 CDT)
  • AMBER: NCOPY definition (Fri Jan 28 2005 - 16:59:14 CST)
• Kevin Murphy
  • AMBER: addles question (Wed Aug 31 2005 - 16:46:00 CDT)
• khn _
  • AMBER: ew_bspline.h error (Wed Aug 17 2005 - 22:33:08 CDT)
• Kitiyaporn Wittayanarakul
  • AMBER: How to add water to calculate MMPBSA (Wed Dec 14 2005 - 12:06:53 CST)
• kkirschn_at_hamilton.edu
  • AMBER: Clustering - MMTSB Toolkit kclust (Wed Dec 07 2005 - 12:43:52 CST)
  • Re: AMBER: RMSD Calculations (Mon Dec 05 2005 - 10:29:23 CST)
  • Re: AMBER: Glycam-parameters and antechamber (Tue Sep 20 2005 - 15:37:16 CDT)
  • Re: AMBER: building monosaccharides with glycam force field (Tue Sep 20 2005 - 14:12:33 CDT)
  • Re: AMBER: glycan (Wed Aug 17 2005 - 14:55:35 CDT)
• Knut Langsetmo
  • Re: AMBER: Making movie from AMBER trajectory (Mon Nov 07 2005 - 12:42:08 CST)
• konnipati murali
  • AMBER: Hi..I am new to AMBER.(compilation with MPICH-G2 libraries)... (Sun Oct 23 2005 - 01:38:28 CDT)
• Kristof Stevens
  • AMBER: AMBER7 xleap problem (Thu Sep 22 2005 - 06:00:54 CDT)
  • AMBER: power supply crash==>boot problems (Wed Aug 03 2005 - 03:20:08 CDT)
• kuljeets_at_igib.res.in
  • Re: AMBER: average structure after MD (Thu May 26 2005 - 00:42:32 CDT)
  • AMBER: average structure after MD (Wed May 25 2005 - 04:14:19 CDT)
• L Jin
  • Re: AMBER: Modeling of a radical (Mon Aug 01 2005 - 08:50:55 CDT)
  • AMBER: Modeling of a radical (Thu Jul 14 2005 - 05:46:20 CDT)
  • Re: AMBER: Error on restrained MD equilibration (AMBER 7) (Wed Jun 01 2005 - 10:05:12 CDT)
  • RE: AMBER: Error on restrained MD equilibration (AMBER 7) (Wed Jun 01 2005 - 05:20:40 CDT)
  • Re: AMBER: Error on restrained MD equilibration (AMBER 7) (Wed Jun 01 2005 - 05:24:12 CDT)
  • Re: AMBER: Error on restrained MD equilibration (AMBER 7) (Tue May 31 2005 - 11:21:55 CDT)
  • AMBER: Error on restrained MD equilibration (AMBER 7) (Tue May 31 2005 - 10:23:51 CDT)
  • Re: AMBER: Restraint of atoms during minimization (Tue Feb 22 2005 - 11:12:13 CST)
  • AMBER: Restraint of atoms during minimization (Tue Feb 22 2005 - 10:17:05 CST)
  • AMBER: Phi-Psi-Energy plot (Wed Feb 16 2005 - 09:45:18 CST)
• L.C. Heady
  • AMBER: Saturated DNA bases (Wed Jun 01 2005 - 03:55:54 CDT)
• Lars Packschies
  • AMBER: just one more try:) xleap, opteron, pgi and segmentation fault. (fwd) (Fri Nov 04 2005 - 06:09:40 CST)
  • AMBER: xleap, opteron, pgi and segmentation fault. (Wed Oct 26 2005 - 08:57:40 CDT)
  • Re: AMBER: parallel AMBER/pmemd installation problem on Opteron (Thu Feb 24 2005 - 17:58:25 CST)
  • Re: AMBER: parallel AMBER/pmemd installation problem on Opteron (Wed Feb 23 2005 - 10:22:59 CST)
• Latifa Douali
  • AMBER: TI calculation using sander (Tue Jun 07 2005 - 19:10:54 CDT)
• laura zan
  • AMBER: RESP problem RESP (Mon Nov 14 2005 - 07:54:28 CST)
• Lauren O'Neil
  • AMBER: DNA base-flipping: TI vs PMF (Tue May 31 2005 - 10:40:45 CDT)
• Laurence Lavelle
  • AMBER: Protein dynamics. (Wed Jun 08 2005 - 00:52:00 CDT)
  • AMBER: Protein dynamics. (Mon Jun 06 2005 - 16:43:50 CDT)
• Lei Jia
  • AMBER: NMR refinement (Fri Aug 05 2005 - 14:50:29 CDT)
  • Re: AMBER: Sander: idecomp (Tue Mar 15 2005 - 20:25:24 CST)
  • AMBER: Sander: idecomp (Tue Mar 15 2005 - 13:45:47 CST)
  • AMBER: DNA melting free energy calculation (Thu Feb 03 2005 - 18:39:57 CST)
• Li Su
  • AMBER: a problem encountered when trying to equalibrate alanine dipeptide in explicit water (Wed Aug 24 2005 - 12:36:06 CDT)
  • AMBER: How to deal with the problem that a molecule go out the virtual box in vaccum (Tue Aug 23 2005 - 12:37:38 CDT)
  • AMBER: a question about varying positions of dihedral restraints with step number (Wed Jun 22 2005 - 14:42:02 CDT)
  • AMBER: How to turn off pme when using periodic box (Mon Jun 20 2005 - 13:31:09 CDT)
  • AMBER: How to set the virtual box size for a calculation run in vacuum (Mon Jun 20 2005 - 08:27:33 CDT)
  • Re: AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians (Thu Jun 16 2005 - 18:17:46 CDT)
  • AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians (Thu Jun 16 2005 - 16:19:36 CDT)
  • AMBER: How to modify force constants and equalibrium values for standard residues (Thu Jun 16 2005 - 08:30:41 CDT)
  • Re: AMBER: why the dipeptide always moving out the virtual box (Tue Jun 14 2005 - 16:11:41 CDT)
  • AMBER: why the dipeptide always moving out the virtual box (Mon Jun 13 2005 - 16:40:47 CDT)
  • AMBER: How does Amber8 implemnet ntf=4? (Thu Jun 02 2005 - 10:32:30 CDT)
  • Re: AMBER: if setting ntf=4, will it cause someproblem? (Tue May 31 2005 - 16:07:25 CDT)
  • AMBER: if setting ntf=4, will it cause someproblem? (Tue May 31 2005 - 09:55:03 CDT)
  • AMBER: Bond angle restraints setting files (Mon May 30 2005 - 11:05:15 CDT)
  • AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? (Tue May 24 2005 - 14:14:09 CDT)
  • AMBER: How to fix certain bond angles (Tue May 24 2005 - 10:27:14 CDT)
  • AMBER: How to set up dihedral constraints in amber (Mon May 16 2005 - 10:39:50 CDT)
  • AMBER: How to set constraint (Sun May 15 2005 - 13:58:51 CDT)
  • AMBER: Asking how to creat alanine "dipeptide" in amber8 (Wed May 11 2005 - 10:37:07 CDT)
• Lihong Song
  • AMBER: MM-PBSA: plot the "Ggas+Gsol" vs time (Wed Nov 30 2005 - 12:15:28 CST)
• Lihua Wang
  • AMBER: bugfix 49 (Sun Nov 06 2005 - 17:05:20 CST)
  • Re: AMBER: simulation with Mg2+ ions and counter ions (Sat Jul 09 2005 - 03:11:42 CDT)
  • Re: AMBER: transfer data from Linux to windows (Thu Jun 09 2005 - 17:32:14 CDT)
  • Re: AMBER: parameters in gaff.dat (Fri Apr 15 2005 - 13:50:04 CDT)
  • AMBER: parameters in gaff.dat (Fri Apr 15 2005 - 00:21:29 CDT)
  • Re: AMBER: Two question about dielectric constant (Mon Apr 11 2005 - 12:04:24 CDT)
  • Re: AMBER: combine mdcrd using ptraj (Thu Apr 07 2005 - 02:45:18 CDT)
  • AMBER: atom type designation (Fri Mar 04 2005 - 18:05:10 CST)
  • Re: AMBER: amber8 and moil-view (Thu Feb 17 2005 - 14:14:04 CST)
  • Re: AMBER: amber8 and moil-view (Thu Feb 17 2005 - 13:52:08 CST)
  • AMBER: amber8 and moil-view (Thu Feb 17 2005 - 13:26:32 CST)
  • Re: AMBER: running shell scripts in tleap? (Mon Feb 14 2005 - 17:26:31 CST)
  • AMBER: eedmeth=5 (Fri Jan 21 2005 - 18:20:59 CST)
• Lina Nilsson
  • AMBER: building monosaccharides with glycam force field (Tue Sep 20 2005 - 11:09:41 CDT)
  • AMBER: implementing AMBER in NAMD (Thu Apr 28 2005 - 09:23:16 CDT)
  • AMBER: how to make a nonsymmetric box around the solute (Tue Apr 05 2005 - 02:56:44 CDT)
• Linchen Gong
  • AMBER: question about grid in ptraj (Thu Oct 06 2005 - 08:03:00 CDT)
  • RE: RE: Re: AMBER: a trivial question (Fri Aug 05 2005 - 21:52:39 CDT)
  • RE: RE: Re: AMBER: a trivial question (Fri Aug 05 2005 - 21:52:39 CDT)
  • RE: Re: AMBER: a trivial question (Fri Aug 05 2005 - 10:26:25 CDT)
  • AMBER: a trivial question (Thu Aug 04 2005 - 04:14:04 CDT)
  • RE: Re: AMBER: Minimized structure (Thu Jul 28 2005 - 01:55:05 CDT)
• Linda Hooks
  • The new ganaration of repliccas is here capella (Mon May 09 2005 - 20:53:45 CDT)
• Linda Prengaman
  • Re: AMBER: Question about Lennard-Jones Parameters in Topology file (Tue Jul 05 2005 - 12:40:44 CDT)
  • AMBER: Question about Lennard-Jones Parameters in Topology file (Sat Jul 02 2005 - 13:15:51 CDT)
• linfu
  • AMBER: about antechamber(amber8) (Thu Dec 15 2005 - 01:51:16 CST)
• Lishan Yao
  • Re: AMBER: restart file and crd file (Thu Oct 27 2005 - 13:59:29 CDT)
  • Re: AMBER: restart file and crd file (Thu Oct 27 2005 - 12:54:26 CDT)
  • Re: AMBER: restart file and crd file (Thu Oct 27 2005 - 12:03:58 CDT)
  • Re: AMBER: restart file and crd file (Thu Oct 27 2005 - 10:50:15 CDT)
  • Re: AMBER: restart file and crd file (Thu Oct 27 2005 - 10:33:20 CDT)
  • AMBER: restart file and crd file (Thu Oct 27 2005 - 08:37:29 CDT)
  • AMBER: roar question (Thu Sep 15 2005 - 20:08:37 CDT)
• Liu, Jingyuan
  • AMBER: Protonate state of ARG and LYS. (Thu Feb 10 2005 - 15:56:39 CST)
• Lorna Stimson
  • Re: AMBER: sp0 console message after using addAtomTypes (Tue Nov 22 2005 - 11:04:07 CST)
  • AMBER: Using OPLS atom types (Tue Nov 22 2005 - 10:18:48 CST)
  • AMBER: sp0 console message after using addAtomTypes (Tue Nov 22 2005 - 02:44:19 CST)
• luaj_at_sohu.com
  • AMBER: how can I constitute T-phosphotyrosine group ? (Wed Oct 12 2005 - 23:50:16 CDT)
  • AMBER: how can I constitute T-phosphotyrosine group ? (Tue Oct 11 2005 - 09:25:02 CDT)
  • AMBER: how to constitute T-phosphotyrosine group? (Tue Oct 11 2005 - 07:28:38 CDT)
• luckyang_at_gmail.com
  • AMBER: antechamber problem using RESP (Mon Aug 01 2005 - 20:29:26 CDT)
  • Re: AMBER: (Fri May 20 2005 - 13:28:17 CDT)
  • AMBER: Silicon related parameters (Tue Apr 12 2005 - 11:38:35 CDT)
  • Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' (Wed Mar 23 2005 - 17:01:49 CST)
  • Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' (Wed Mar 23 2005 - 16:18:45 CST)
  • Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' (Tue Mar 22 2005 - 18:46:26 CST)
  • AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' (Tue Mar 22 2005 - 17:34:05 CST)
• Lukasz Bielecki
  • AMBER: My model loses its motion in MD (Thu Nov 24 2005 - 09:06:14 CST)
  • AMBER: stripwater (Wed Jun 01 2005 - 09:16:05 CDT)
  • Re: Re :AMBER: Holes in water (Sat Mar 12 2005 - 10:52:31 CST)
  • AMBER: Holes in water (Fri Mar 11 2005 - 08:13:40 CST)
• lv haiting
  • Re: AMBER: lib-4324 : UNRECOVERABLE library error (Wed Dec 21 2005 - 22:21:50 CST)
  • AMBER: lib-4324 : UNRECOVERABLE library error (Wed Dec 21 2005 - 20:31:46 CST)
  • AMBER: How to deal with the Non-standard residue (Mon Apr 25 2005 - 03:18:08 CDT)
  • Re: AMBER: ATTN REVISION (Tue Apr 19 2005 - 21:08:14 CDT)
• Lwin, ThuZar
  • AMBER: structures extracted from mmpbsa (Fri Aug 19 2005 - 18:25:44 CDT)
  • AMBER: how is truncated octahedron box calculated (Thu Jul 07 2005 - 15:38:05 CDT)
  • AMBER: problem with addIons (Wed Jul 06 2005 - 16:41:25 CDT)
  • AMBER: box size in explicit water (Wed Jul 06 2005 - 11:39:47 CDT)
  • AMBER: setting up restraint with ntr option (Thu Jun 09 2005 - 16:49:04 CDT)
  • AMBER: GB/SA/LD parallel sander (Wed Jun 08 2005 - 14:36:41 CDT)
  • AMBER: GB/SA/LD parallel sander (Mon Jun 06 2005 - 11:48:27 CDT)
• m m
  • AMBER: Amber 8 with lam compilation problem (Mon Feb 21 2005 - 02:55:49 CST)
• M. L. Dodson
  • Re: AMBER: [OT] A nab programming question (Tue Jul 26 2005 - 09:32:47 CDT)
  • AMBER: [OT] A nab programming question (Thu Jul 21 2005 - 15:07:09 CDT)
  • Re: AMBER: Amber8 Solaris installation failure (Mon Feb 28 2005 - 14:55:47 CST)
  • Re: AMBER: Amber8 Solaris installation failure (Tue Feb 22 2005 - 20:33:31 CST)
  • Re: AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) (Thu Feb 17 2005 - 20:21:29 CST)
  • Re: AMBER: Convert to Pdb (Wed Feb 09 2005 - 13:28:22 CST)
  • Re: AMBER: Multiple dihedral restraints (follow up) (Thu Feb 03 2005 - 14:07:11 CST)
  • Re: AMBER: Floating Exception and installation on Digital Unix. (Tue Jan 11 2005 - 09:46:45 CST)
  • Re: AMBER: Questions about sander.QMMM (Fri Jan 07 2005 - 10:45:45 CST)
  • Re: AMBER: Questions about sander.QMMM (Fri Jan 07 2005 - 10:26:25 CST)
• M. Scott Shell
  • AMBER: D-enantiomers (Tue Sep 20 2005 - 13:43:03 CDT)
• Maciej
  • AMBER: Trouble with example tutorial (Wed May 11 2005 - 06:08:02 CDT)
  • AMBER: Problem with "Thermodynamic integration calculations" tutorial ,unsuspected error (Thu Apr 28 2005 - 02:41:21 CDT)
  • AMBER: Re:Gibbs compilation problem (Tue Apr 26 2005 - 02:05:31 CDT)
  • AMBER: Free energy (Tue Apr 26 2005 - 02:01:16 CDT)
  • AMBER: Gibbs compilation problem (Tue Apr 19 2005 - 06:36:52 CDT)
  • AMBER: New parametrs (Tue Apr 19 2005 - 00:38:51 CDT)
  • AMBER: A few question about RDF input preparation (Thu Mar 24 2005 - 05:13:10 CST)
  • AMBER: Could not open file (trajin) with mode (r) (Wed Mar 23 2005 - 07:52:20 CST)
  • AMBER: RDF input preparation problem (Sun Mar 13 2005 - 22:12:22 CST)
  • Re: AMBER: Amber 8 on cygwin install problem (Fri Mar 04 2005 - 00:51:32 CST)
  • AMBER: Amber 8 on cygwin install problem (Thu Mar 03 2005 - 04:49:17 CST)
  • Re: AMBER: Installation problem (Thu Mar 03 2005 - 03:26:30 CST)
  • AMBER: How to build dynamics input for guanine with tleap ? (Thu Feb 24 2005 - 07:44:37 CST)
  • AMBER: RE:Amber 8 with lam compilation problem (Thu Feb 24 2005 - 01:43:53 CST)
• Maciej KA
  • AMBER: RE:Amber 8 with lam compilation problem (Wed Feb 23 2005 - 02:07:37 CST)
  • AMBER: RE:Amber 8 with lam compilation problem (Wed Feb 23 2005 - 01:08:16 CST)
• Madjid Taghdir
  • AMBER: Can I trust ANAL result? (Tue Oct 04 2005 - 05:55:51 CDT)
  • AMBER: solvation energy (Wed Sep 07 2005 - 05:08:31 CDT)
  • AMBER: cutoff in ANAL (Wed Jul 27 2005 - 03:06:54 CDT)
• Magne Olufsen
  • Re: AMBER: MM_PBSA problem (Fri Nov 04 2005 - 01:50:30 CST)
  • AMBER: mm_pbsa: problems with dielec constant when using (Thu Sep 15 2005 - 06:02:35 CDT)
  • AMBER: molsurf: problem with calculate surface area (Fri Aug 12 2005 - 03:06:45 CDT)
• Majid moghaddam
  • Re: AMBER: I am looking forward to hearing from you. (Wed Oct 26 2005 - 05:18:58 CDT)
  • AMBER: RMS fluctuations along modes obtained from PCA (Mon Jan 17 2005 - 07:47:56 CST)
• Manish Datt
  • Re: AMBER: problem with temperature weights (Fri Oct 07 2005 - 23:50:07 CDT)
  • AMBER: problem with temperature weights (Fri Oct 07 2005 - 10:43:52 CDT)
• Marc Baaden
  • Re: AMBER: Metals with Amber (Thu Nov 03 2005 - 06:33:34 CST)
  • Re: AMBER: Question about Prep file (Fri Jul 22 2005 - 01:38:42 CDT)
  • AMBER: Bio-Image summer school in Paris this year (Wed Mar 16 2005 - 05:44:47 CST)
  • Re: AMBER: Sample more conformational space (Wed Mar 02 2005 - 07:03:02 CST)
• Marc Christensen
  • AMBER: Antechamber/Divcon assigned charges (Thu Mar 03 2005 - 21:38:10 CST)
• Marc Petitmermet
  • AMBER: Compiling on dual-opteron with pathscale 2.1 on RHEL 4 AS (Thu Mar 31 2005 - 09:32:31 CST)
  • Re: AMBER: compiler for amber8 on opteron (Fri Mar 18 2005 - 02:22:42 CST)
  • AMBER: compiler for amber8 on opteron (Thu Mar 17 2005 - 09:56:37 CST)
• Marcela Madrid
  • AMBER: warning in leap (Tue Oct 11 2005 - 16:26:42 CDT)
• Marcin Krol
  • Re: AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" (Tue May 31 2005 - 11:17:30 CDT)
• Marie-Pierre Durrieu
  • Re: AMBER: problem with ptraj and randomizeions (Fri Feb 18 2005 - 04:19:06 CST)
  • Re: AMBER: problem with ptraj and randomizeions (Fri Feb 18 2005 - 03:49:16 CST)
  • AMBER: too much vacuum in the box created by Leap (Fri Feb 11 2005 - 06:53:35 CST)
  • AMBER: vacuum bubbles in system equilibration (Tue Feb 01 2005 - 04:56:21 CST)
• Marios Constantinou
  • AMBER: problems installing amber 7 on a RH Linux 8 machine (Thu Oct 27 2005 - 10:28:00 CDT)
• Mark H. Schofield
  • AMBER: compilation problem (Mac OS X.4) (Fri Aug 26 2005 - 11:07:05 CDT)
• Mark Rance
  • Re: AMBER: AMBER8 Build on Linux x64 running Opterons (Wed May 11 2005 - 10:02:05 CDT)
• Mark Williamson
  • Re: AMBER: Simple 3D Molecule Visualization (Tue Oct 18 2005 - 11:50:07 CDT)
  • Re: AMBER: problem with xleap (Tue Oct 18 2005 - 09:04:43 CDT)
  • Re: AMBER: Installation problem. . (Thu Jun 16 2005 - 10:15:58 CDT)
  • Re: AMBER: Installation problem. . (Thu Jun 16 2005 - 10:06:57 CDT)
  • Re: AMBER: Vibrational spectrum? [SOLUTION] (Fri Jun 10 2005 - 05:33:51 CDT)
• Markus W. Germann
  • AMBER: Xserve and amber (Mon Mar 14 2005 - 10:55:53 CST)
  • Re: AMBER: Amber7 nmropt (Wed Feb 16 2005 - 15:40:46 CST)
  • AMBER: Amber7 nmropt (Wed Feb 16 2005 - 15:09:08 CST)
• marti
  • Re: AMBER: Use of ibelly with nmode analysis (Thu Feb 24 2005 - 05:47:28 CST)
• Martin Sippel
  • Re: AMBER: Free energy calculation for protein-protein complex usingMM_PBSA (Thu Jun 30 2005 - 05:32:11 CDT)
  • Re: AMBER: nmode with ibelly (Wed Jun 08 2005 - 12:48:04 CDT)
  • Re: AMBER: nmode with ibelly (Tue Jun 07 2005 - 05:11:44 CDT)
  • AMBER: nmode with ibelly (Mon Jun 06 2005 - 04:38:42 CDT)
  • AMBER: Nmode calculations (Fri Jun 03 2005 - 12:17:48 CDT)
  • AMBER: Nmode with residues excluded (Fri Jun 03 2005 - 11:56:42 CDT)
• masi_at_nmr.mpibpc.mpg.de
  • AMBER: STOP 0 (Tue May 31 2005 - 11:40:25 CDT)
  • AMBER: MM-PBSA calculation (Tue May 31 2005 - 11:37:40 CDT)
• mathew k varghese
  • AMBER: cluster analysis (Wed Nov 23 2005 - 01:03:27 CST)
  • Re: AMBER: ptraj Hbond analysis (Sat Nov 19 2005 - 05:36:12 CST)
  • Re: AMBER: ptraj Hbond analysis (Thu Nov 17 2005 - 22:09:14 CST)
  • AMBER: ptraj Hbond analysis (Wed Nov 16 2005 - 22:28:52 CST)
  • Re: AMBER: (no subject) (Thu Oct 20 2005 - 03:31:21 CDT)
  • AMBER: (no subject) (Thu Oct 20 2005 - 00:19:06 CDT)
  • Re: AMBER: Equillibration run (Fri Sep 09 2005 - 08:16:24 CDT)
  • AMBER: Equillibration run (Fri Sep 09 2005 - 01:40:08 CDT)
  • AMBER: Equilibration MD (Sat Sep 03 2005 - 00:55:22 CDT)
  • AMBER: nucgen error (U not generated) (Wed Jul 27 2005 - 22:28:51 CDT)
  • AMBER: Error in MD (Thu Jul 21 2005 - 22:53:08 CDT)
  • Re: AMBER: AMBER-process_mdout.perl (Mon Jul 18 2005 - 06:22:56 CDT)
  • Re: AMBER: building nucleic acids (Sat Jul 09 2005 - 00:55:00 CDT)
  • AMBER: building nucleic acids (Thu Jul 07 2005 - 23:07:03 CDT)
  • AMBER: setting up Parallel processing (Thu May 26 2005 - 10:39:00 CDT)
  • AMBER: distance restraints (Thu Apr 28 2005 - 02:00:16 CDT)
  • Re: AMBER: rst file problems (Mon Apr 11 2005 - 22:13:21 CDT)
  • AMBER: rst file problems (Mon Apr 11 2005 - 05:03:41 CDT)
  • AMBER: value of SALTCON (Wed Apr 06 2005 - 23:29:01 CDT)
  • AMBER: GB dynamics (Thu Mar 31 2005 - 22:01:30 CST)
  • AMBER: leap warnings (Mon Mar 14 2005 - 00:34:32 CST)
  • AMBER: amber on sgi (Wed Mar 09 2005 - 05:23:12 CST)
  • AMBER: size of solventbox (Tue Feb 22 2005 - 22:07:00 CST)
• Matthew Davies
  • AMBER: mm_pbsa question (Tue Jul 19 2005 - 05:07:51 CDT)
• Mayumi Haga
  • AMBER: ptraj problem (Tue Feb 22 2005 - 03:38:43 CST)
  • RE: AMBER: AIX problem (Mon Feb 21 2005 - 18:45:33 CST)
  • AMBER: AIX problem (Sun Feb 20 2005 - 23:17:29 CST)
  • AMBER: How to calculate RESTRAINT value (Mon Feb 07 2005 - 22:09:25 CST)
  • AMBER: How to make PDB file by myself (Mon Jan 24 2005 - 22:23:32 CST)
• mcpreto_at_fc.up.pt
  • Re: AMBER: average struct without solvent (Mon Nov 21 2005 - 08:20:39 CST)
• Megan G
  • AMBER: oxidised methionine residue (Fri Oct 14 2005 - 10:45:21 CDT)
• Mehdi Davari
  • AMBER: I am looking forward to hearing from you. (Tue Oct 25 2005 - 13:38:28 CDT)
• Melinda Layten
  • Re: Re: AMBER: REMD error!!! (Fri Oct 28 2005 - 10:26:46 CDT)
  • Re: AMBER: restart file and crd file (Thu Oct 27 2005 - 13:35:54 CDT)
  • Re: AMBER: Invalid Digit "*" (Wed Sep 28 2005 - 14:17:29 CDT)
  • Re: AMBER: How to split LES trajectory using TRAJ (Wed Sep 21 2005 - 15:09:29 CDT)
  • Re: AMBER: Could not open file (Melb.mdcrd) with mode (r) (Mon Sep 19 2005 - 12:00:51 CDT)
  • Re: AMBER: box size in explicit water (Wed Jul 06 2005 - 11:52:55 CDT)
  • Re: AMBER: Making topology files of big moleucles in antechamber (Thu Mar 17 2005 - 13:48:39 CST)
  • Re: AMBER: Trajectory problems (Thu Mar 17 2005 - 13:34:50 CST)
  • Re: AMBER: amber on sgi (Wed Mar 09 2005 - 10:52:28 CST)
  • Re: AMBER: Problem with restart file (Thu Jan 13 2005 - 08:53:42 CST)
• Mengjuei Hsieh
  • Re: AMBER: Xserve and amber (Mon Mar 14 2005 - 19:51:12 CST)
• Mey Khalili
  • Re: AMBER: Separating solvent and solute energy in the microcanonical mode (Thu Mar 17 2005 - 17:11:48 CST)
  • AMBER: Separating solvent and solute energy in the microcanonical mode (Thu Mar 17 2005 - 16:50:09 CST)
• mfyang
  • AMBER: GCC for AMBER on 64 bit machine (Thu Jun 23 2005 - 12:55:01 CDT)
• michael chen
  • AMBER: Disulfide bond (Fri Apr 08 2005 - 09:36:41 CDT)
  • AMBER: question about surface area to GBsurf calculation (Thu Feb 10 2005 - 00:20:58 CST)
  • AMBER: Another question about surface area calculation (Thu Feb 10 2005 - 00:26:00 CST)
  • AMBER: question about mm_gbsa output file (Wed Feb 09 2005 - 12:10:06 CST)
• Michael Crowley
  • Re: AMBER: ew_bspline.h error (Fri Aug 19 2005 - 10:54:39 CDT)
  • Re: AMBER: nonbond_list question . (Sat Jun 18 2005 - 14:51:01 CDT)
  • Re: AMBER: SANDER BOMB: volume of ucell too big (Thu May 12 2005 - 12:10:20 CDT)
  • Re: AMBER: maximum number of processors (Thu May 12 2005 - 12:00:09 CDT)
• Michael Dolan
  • Re: AMBER: params for cofactors (Mon Aug 29 2005 - 15:23:10 CDT)
  • AMBER: params for cofactors (Mon Aug 29 2005 - 14:54:41 CDT)
• Michael Mazanetz
  • AMBER: FATAL error with ATP and MG2 - fixed (Thu Nov 17 2005 - 06:45:27 CST)
  • AMBER: FATAL error with ATP, MG2 residue (Thu Nov 17 2005 - 03:41:12 CST)
• Michele Porro
  • AMBER: Glycam-parameters and antechamber (Wed Sep 14 2005 - 11:06:42 CDT)
• milion_at_c-box.cz
  • AMBER: Vibrational spectrum? (Fri Jun 10 2005 - 03:31:27 CDT)
  • AMBER: GB - igb=1 versus dielc=? (Thu May 19 2005 - 03:36:34 CDT)
• mingche Pan
  • Re: AMBER: Mg2+ issues of using MM-PB/GBSA (Fri Dec 02 2005 - 13:36:53 CST)
  • Re: AMBER: Mg2+ issues of using MM-PB/GBSA (Fri Dec 02 2005 - 12:09:28 CST)
  • Re: AMBER: Mg2+ issues of using MM-PB/GBSA (Fri Dec 02 2005 - 10:32:15 CST)
  • AMBER: Mg2+ issues of using MM-PB/GBSA (Thu Dec 01 2005 - 13:01:24 CST)
  • AMBER: molsurf error (Tue May 17 2005 - 11:52:57 CDT)
  • Re: AMBER: error in pbsa calculation (Wed Apr 27 2005 - 11:20:10 CDT)
  • AMBER: error in pbsa calculation (Tue Apr 26 2005 - 16:15:13 CDT)
  • RE: AMBER: nmode calculation (Mon Jan 24 2005 - 16:12:13 CST)
  • AMBER: nmode calculation (Mon Jan 24 2005 - 09:34:18 CST)
  • AMBER: nmode calculation (Fri Jan 21 2005 - 19:43:32 CST)
• Mingfeng Yang
  • Re: AMBER: Making movie from AMBER trajectory (Tue Nov 08 2005 - 10:01:52 CST)
  • AMBER: tkbc2 (Mon Oct 31 2005 - 16:59:17 CST)
  • Re: AMBER: restart file and crd file (Thu Oct 27 2005 - 14:40:51 CDT)
  • Re: AMBER: restart file and crd file (Thu Oct 27 2005 - 11:11:16 CDT)
  • Re: AMBER: Simple 3D Molecule Visualization (Wed Oct 19 2005 - 13:19:01 CDT)
  • Re: AMBER: Simple 3D Molecule Visualization (Wed Oct 19 2005 - 13:19:18 CDT)
  • Re: AMBER: Installation error - icc: command not found (Wed Oct 05 2005 - 09:14:16 CDT)
  • AMBER: Amber compilation on opteron with PGI compiler (Fri Sep 30 2005 - 08:15:43 CDT)
  • AMBER: Minimization in sander and nmode (Thu Sep 29 2005 - 18:01:24 CDT)
  • AMBER: Leap compilation with pgf77 under 64bit platform (Wed Sep 21 2005 - 16:09:39 CDT)
  • AMBER: Target MD and nmode test hang (Thu Mar 31 2005 - 20:08:13 CST)
• Mingyue Zheng
  • Re: AMBER: What PRESS is? (Mon Mar 07 2005 - 21:26:01 CST)
• mk mk
  • AMBER: GNU Autotool integration for Amber8! (Sun Oct 16 2005 - 02:06:11 CDT)
• mmv
  • AMBER: mean structure calculation (Fri Apr 22 2005 - 04:17:20 CDT)
• mmv_at_whu.edu.cn
  • AMBER: All the tests passed except prmtop and prepin... (Thu Mar 31 2005 - 03:59:26 CST)
• Mohammed Mayeed
  • AMBER: Protein-surface interaction (Wed Jun 08 2005 - 13:37:30 CDT)
  • AMBER: (no subject) (Wed Jun 08 2005 - 12:26:15 CDT)
• Monica Civera
  • AMBER: Temperature regulation (Tue Aug 30 2005 - 09:43:26 CDT)
  • AMBER: GAFF angle parameters (Tue May 17 2005 - 11:11:46 CDT)
  • AMBER: units (Wed Jan 12 2005 - 09:12:19 CST)
  • AMBER: van der waals parameters (Wed Jan 12 2005 - 05:42:53 CST)
  • AMBER: guanidinium chloride (Mon Jan 10 2005 - 09:27:38 CST)
• Morena Spreafico
  • AMBER: parameters for fluorine atom (Thu Dec 15 2005 - 06:33:52 CST)
• mrbroad_at_ilstu.edu
  • AMBER: Free Energy Calculation torsion missing (Tue Jun 14 2005 - 13:21:54 CDT)
  • AMBER: Free energy pertubation (thermodynamic intergration) (Mon Apr 25 2005 - 11:20:35 CDT)
  • AMBER: loading pdb in leap to create parmeter files (Sat Feb 05 2005 - 15:24:04 CST)
• MURAT CETINKAYA
  • Re: AMBER: amber8 parallel sander (Mon Oct 03 2005 - 21:04:04 CDT)
  • AMBER: MM-PBSA error (Mon Sep 05 2005 - 11:00:13 CDT)
  • RE: AMBER: installing amber7 on 64bit cluster (Thu Aug 04 2005 - 10:04:47 CDT)
  • AMBER: installing amber7 on 64bit cluster (Wed Aug 03 2005 - 10:46:20 CDT)
  • AMBER: maximum number of processors (Wed May 11 2005 - 22:53:44 CDT)
• myang
  • Re: AMBER: protonate (Tue Jan 18 2005 - 10:07:12 CST)
• Myra Cole
  • FW: Office XP - 60 dolars! coagulate (Tue May 17 2005 - 19:04:52 CDT)
• Myunggi Yi
  • AMBER: radial distribution function (Mon May 09 2005 - 13:36:43 CDT)
  • Re: AMBER: How can I read parm99.dat file? (Fri May 06 2005 - 08:18:47 CDT)
  • Re: AMBER: How can I read parm99.dat file? (Fri May 06 2005 - 09:14:15 CDT)
  • Re: AMBER: How can I read parm99.dat file? (Fri May 06 2005 - 09:14:04 CDT)
  • AMBER: How can I read parm99.dat file? (Wed May 04 2005 - 18:08:49 CDT)
  • AMBER: Can I add iodide anione? (Tue May 03 2005 - 12:36:07 CDT)
• Nadine Homeyer
  • AMBER: Parameters for phosphorylated amino acids (Thu Jun 23 2005 - 09:24:08 CDT)
  • AMBER: Parameters for phosphorylated amino acids (Thu Jun 23 2005 - 08:54:22 CDT)
  • Re: AMBER: Need help in charge fitting through RESP (Mon Jun 13 2005 - 11:20:49 CDT)
• nadtanet
  • AMBER: Manganese ion parameter (Tue Oct 04 2005 - 06:55:59 CDT)
• nadtanet nunthaboot
  • AMBER: AMBER8 limitation of memory in QM/MM calculation (Mon Aug 01 2005 - 21:21:59 CDT)
• nag raj
  • AMBER: ESP exceeds the MAXESP(20000), (Thu Nov 10 2005 - 04:36:37 CST)
  • AMBER: How to construct a lipid bilayer (Fri Aug 19 2005 - 00:01:06 CDT)
  • AMBER: Atom type problem (Thu Aug 11 2005 - 09:18:31 CDT)
  • AMBER: How to insert a protein in lipid bilayer (Wed Jul 27 2005 - 11:56:07 CDT)
  • AMBER: Lipid parameters (Tue Jul 26 2005 - 05:55:22 CDT)
  • AMBER: Lipid bilayer parameters and charmm force field parameters (Fri Jul 22 2005 - 22:15:35 CDT)
  • AMBER: Lipid bilayer parameters (Fri Jul 22 2005 - 02:18:24 CDT)
• Nagy, Peter I.
  • RE: AMBER: guanidinium chloride (Mon Jan 10 2005 - 11:15:41 CST)
• nallen_at_unca.edu
  • AMBER: Compiling AMBER 8 for Mac OSX (Parallel) (Mon Jan 17 2005 - 11:41:06 CST)
• Natasja Brooijmans
  • Re: AMBER: problem in minimization (Tue Feb 08 2005 - 13:56:22 CST)
• Nelson Fonseca
  • Re: AMBER: installation on a dual core (Fri Dec 16 2005 - 08:14:22 CST)
  • AMBER: MM_PBSA parameters (Tue Dec 06 2005 - 09:26:55 CST)
  • Re: AMBER: MM-PBSA: plot the "Ggas+Gsol" vs time (Wed Nov 30 2005 - 15:33:09 CST)
  • AMBER: MM-PBSA and 1-4 nonbonded interactions (Wed Aug 31 2005 - 09:55:31 CDT)
  • Re: AMBER: MMPBSA calculations on Highly charged systems (Tue May 17 2005 - 07:36:16 CDT)
  • AMBER: strange mm_pbsa.pl bug (Mon May 16 2005 - 10:39:21 CDT)
  • AMBER: PB Bomb in circle(): Stored surface points over limit (Fri Apr 22 2005 - 07:56:57 CDT)
  • Re: AMBER: GB and mm_pbsa.pl (Wed Apr 20 2005 - 11:05:12 CDT)
  • AMBER: GB and mm_pbsa.pl (Wed Apr 20 2005 - 06:48:48 CDT)
  • Re: AMBER: MM_PBSA problem (Tue Apr 12 2005 - 16:15:00 CDT)
  • Re: AMBER: MM_PBSA problem (Tue Apr 12 2005 - 11:20:53 CDT)
  • AMBER: Error limits of TI and MM_PBSA methods (Tue Mar 08 2005 - 10:54:42 CST)
  • AMBER: PB dynamics (Wed Jan 12 2005 - 04:06:33 CST)
  • AMBER: MM_PBSA arguments for MM calculations (Wed Jan 05 2005 - 05:54:30 CST)
• Nikhil Kelshikar \(nkelshik\)
  • AMBER: Interpreting Amber8 Benchmark Results (Wed Aug 31 2005 - 12:07:24 CDT)
• Nina Fischer
  • AMBER: dielectric constant (Mon Apr 18 2005 - 03:22:34 CDT)
• Nitin Bhardwaj
  • AMBER: Adding/recognizing calcium atoms (Wed Dec 07 2005 - 15:24:38 CST)
  • Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list (Tue Nov 15 2005 - 18:11:31 CST)
  • Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list (Fri Nov 11 2005 - 10:25:52 CST)
  • Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list (Thu Nov 10 2005 - 11:13:33 CST)
  • Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list (Thu Nov 10 2005 - 10:40:21 CST)
  • AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list (Wed Nov 09 2005 - 18:55:41 CST)
  • Re: AMBER: Unknown atomtypes in amber (Sat Oct 29 2005 - 14:24:04 CDT)
  • AMBER: Unknown atomtypes in amber (Thu Oct 27 2005 - 12:26:49 CDT)
  • Re: AMBER: Antechamber error (Tue Oct 25 2005 - 19:16:20 CDT)
  • AMBER: Antechamber error (Tue Oct 25 2005 - 18:27:39 CDT)
  • Re: AMBER: parmchk error : Cannot open CONNECT.TPL, exit (Tue Oct 25 2005 - 16:52:32 CDT)
  • AMBER: parmchk error : Cannot open CONNECT.TPL, exit (Tue Oct 25 2005 - 16:08:02 CDT)
  • AMBER: Parameters and topology for Diacylglycerol (DAG) (Mon Oct 10 2005 - 13:02:14 CDT)
  • AMBER: antechamber + mopac failure (Mon Sep 19 2005 - 11:36:30 CDT)
  • AMBER: creating a resp input file without Gaussian. (Mon Sep 19 2005 - 11:37:29 CDT)
  • AMBER: creating a respgen file without Gaussian. (Thu Sep 15 2005 - 15:08:36 CDT)
  • AMBER: antechamber + mopac failure (Thu Sep 15 2005 - 14:59:27 CDT)
  • AMBER: Parameter files for general lipids (Mon Mar 28 2005 - 18:57:46 CST)
• nlxc
  • AMBER: antechamber for cyano group (Thu Apr 14 2005 - 13:03:35 CDT)
• Noriyuki Yamaotsu
  • Re: AMBER: compiler for amber8 on opteron (Thu Mar 17 2005 - 19:50:24 CST)
• Oliver Hucke
  • Re: AMBER: Leap problem (Thu Jul 14 2005 - 20:48:52 CDT)
  • Re: AMBER: TI - frcmod file (Wed Jul 13 2005 - 16:18:08 CDT)
  • Re: AMBER: TI - frcmod file (Tue Jul 12 2005 - 18:54:11 CDT)
  • AMBER: TI - frcmod file (Tue Jul 12 2005 - 14:21:44 CDT)
  • AMBER: puzzling gaff parameter (Tue Jun 14 2005 - 20:16:35 CDT)
  • Re: AMBER: Request for g98 (IOP...) (Tue Jun 14 2005 - 11:20:51 CDT)
  • AMBER: gaff: ca-ca-c -o torsion parameter (Tue May 17 2005 - 15:54:24 CDT)
  • Re: AMBER: Protein with structural ions (Tue Apr 05 2005 - 16:42:29 CDT)
• online-banking-rep4958_at_bankofthewest.com
  • Bank of the West Alert (Wed Aug 24 2005 - 03:27:44 CDT)
• opitz_at_che.udel.edu
  • AMBER: ptraj command inputs (Wed Aug 10 2005 - 17:29:34 CDT)
  • AMBER: ptraj help, how to enable disabled ptraj routine? (Mon Aug 01 2005 - 10:19:20 CDT)
  • AMBER: ptraj output missing (Fri Jul 29 2005 - 10:05:19 CDT)
  • Re: AMBER: Question about Prep file (Fri Jul 22 2005 - 14:21:20 CDT)
  • AMBER: Question about Prep file (Thu Jul 21 2005 - 15:52:41 CDT)
  • Re: AMBER: MM_PBSA help, please (Tue Jul 12 2005 - 17:18:50 CDT)
  • Re: AMBER: MM_PBSA help, please (Tue Jul 12 2005 - 12:29:19 CDT)
  • Re: AMBER: MM_PBSA help, please (Tue Jul 12 2005 - 09:19:05 CDT)
  • Re: AMBER: MM_PBSA help, please (Mon Jul 11 2005 - 16:15:19 CDT)
  • AMBER: MM_PBSA help, please (Mon Jul 11 2005 - 10:55:47 CDT)
  • AMBER: question about Carnal (Wed Jun 22 2005 - 15:03:45 CDT)
  • Re: AMBER: atom type question (Mon Jun 13 2005 - 15:46:18 CDT)
  • AMBER: atom type question (Mon Jun 13 2005 - 14:41:30 CDT)
  • AMBER: xleap, lib file question (Wed Apr 13 2005 - 16:36:51 CDT)
  • Re: AMBER: Hydrogen bonding question (Tue Mar 15 2005 - 09:34:53 CST)
  • AMBER: Hydrogen bonding question (Tue Mar 15 2005 - 08:57:45 CST)
  • Re: AMBER: Question about radial command in ptraj (Mon Mar 14 2005 - 14:04:55 CST)
  • AMBER: Question about radial command in ptraj (Mon Mar 14 2005 - 13:19:11 CST)
  • AMBER: Restart Problem (Mon Feb 14 2005 - 13:12:54 CST)
• Osman Gani
  • AMBER: global pH variation in AMBER. (Tue Mar 08 2005 - 04:56:06 CST)
• Osmar Norberto de Souza
  • AMBER: GBSA and thermodynamic ensemble (Mon Jun 13 2005 - 13:29:18 CDT)
• Ozlem Demir
  • AMBER: tyrosyl charges (Thu Jul 07 2005 - 12:07:24 CDT)
• Paramasivam Manikandan
  • AMBER: Request for g98 (IOP...) (Tue Jun 14 2005 - 10:04:30 CDT)
• Pascal Auffinger
  • Re :AMBER: Holes in water (Fri Mar 11 2005 - 09:26:31 CST)
• pascal.baillod_at_epfl.ch
  • AMBER: ptraj - hbond detailed analysis over time? (Thu May 26 2005 - 12:38:38 CDT)
  • AMBER: hbond detailed analysis over time? (Mon May 23 2005 - 13:04:10 CDT)
  • AMBER: langevin, GB and simulated annealing - 5 (Mon May 09 2005 - 11:25:12 CDT)
  • AMBER: langevin, GB and simulated annealing - 4 (Tue Apr 26 2005 - 10:23:20 CDT)
  • AMBER: langevin, GB and simulated annealing - 3 (Tue Apr 26 2005 - 05:37:16 CDT)
  • AMBER: langevin, GB and simulated annealing - 2 (Tue Apr 19 2005 - 16:07:23 CDT)
  • AMBER: langevin, GB and simulated annealing? (Mon Apr 18 2005 - 10:14:08 CDT)
• Paul Beroza
  • RE: AMBER: molsurf error in MM/PBSA calculation (Thu Jul 14 2005 - 18:01:08 CDT)
• Pavan G
  • AMBER: Comparing EELEC from amber and that calculated in the trivial fashion. (Sun Nov 27 2005 - 21:14:48 CST)
  • AMBER: Why are some of the Lennard-Jones coeffs 0 ? (Wed Aug 31 2005 - 12:18:28 CDT)
  • AMBER: Lennard-Jones coeff... (Tue Aug 30 2005 - 15:26:49 CDT)
  • AMBER: Controlling number of water residues... (Tue Mar 01 2005 - 01:14:51 CST)
• Pavan Ghatty
  • AMBER: Warnings as a file (Sun Apr 10 2005 - 23:37:21 CDT)
  • AMBER: What does this mean .. ? (Thu Mar 31 2005 - 13:14:53 CST)
• Peng Tao
  • Re: AMBER: No exchange among replicas in REMD! (Mon Dec 19 2005 - 12:35:24 CST)
  • Re: AMBER: No exchange among replicas in REMD! (Mon Dec 19 2005 - 08:57:30 CST)
  • Re: AMBER: No exchange among replicas in REMD! (Sun Dec 18 2005 - 19:45:03 CST)
  • AMBER: No exchange among replicas in REMD! (Sun Dec 18 2005 - 16:11:06 CST)
  • AMBER: No exchange among replicas in REMD! (Sun Dec 18 2005 - 16:01:28 CST)
  • Re: AMBER: Replica-Exchange MD from AMBER8! (Sat Dec 03 2005 - 14:19:12 CST)
  • Re: AMBER: Replica-Exchange MD from AMBER8! (Sat Dec 03 2005 - 11:13:15 CST)
  • AMBER: Replica-Exchange MD from AMBER8! (Fri Dec 02 2005 - 16:28:27 CST)
  • AMBER: Some explanations of MM_PBSA @DECOMP OUTPUT file? (Thu Dec 01 2005 - 10:35:09 CST)
  • Re: AMBER: MM/PBSA basic questions (Fri Nov 18 2005 - 12:59:39 CST)
  • AMBER: MM/PBSA basic questions (Fri Nov 18 2005 - 09:41:26 CST)
  • AMBER: Ask for helpf to get examples for MM-PBSA with AMBER8 (Thu Nov 03 2005 - 13:45:39 CST)
• peng79_at_email.unc.edu
  • AMBER: please help us on partial charge calculation of PT complex using RESP (Fri Jul 01 2005 - 10:10:31 CDT)
  • AMBER: Geometrical distortion because of charge? (Mon Mar 14 2005 - 12:21:28 CST)
• Peter Anderson
  • AMBER: Problem finding transition state using NMODE (Thu Sep 22 2005 - 07:36:00 CDT)
• Peter Cornish
  • AMBER: Creating protonated cytidine residue (Wed Aug 10 2005 - 09:57:17 CDT)
• Peter Gannett
  • AMBER: ptraj distance mask (Wed Nov 02 2005 - 11:04:48 CST)
  • Re: AMBER: amber8 parallel sander (Thu Sep 22 2005 - 16:18:22 CDT)
  • Re: AMBER: amber8 parallel sander (Thu Sep 22 2005 - 16:15:12 CDT)
  • Re: AMBER: solvation energy (Wed Sep 07 2005 - 08:10:45 CDT)
  • AMBER: ambpdb core dump (Fri Jul 29 2005 - 06:27:46 CDT)
  • Re: AMBER: ptraj-acceptor mask format (Wed Jul 27 2005 - 15:54:50 CDT)
  • AMBER: ptraj-acceptor mask format (Mon Jul 25 2005 - 14:10:47 CDT)
  • Re: AMBER: Modeling of a radical (Sat Jul 23 2005 - 09:21:25 CDT)
  • AMBER: antechamber error (Thu Jun 30 2005 - 14:05:25 CDT)
  • AMBER: error - compiling antechamber (Wed Jun 29 2005 - 14:30:20 CDT)
  • AMBER: compiler error, SGI Octane (Tue Jun 28 2005 - 07:54:35 CDT)
  • AMBER: oxo-heme (Fri Apr 01 2005 - 16:32:47 CST)
  • Re: AMBER: Convert to Pdb (Wed Feb 09 2005 - 13:07:07 CST)
• Peter Varnai
  • AMBER: iwork array for nmr (Mon Nov 14 2005 - 14:20:38 CST)
  • Re: AMBER: REM difficulties (Thu Nov 03 2005 - 13:26:11 CST)
  • AMBER: REM difficulties (Thu Nov 03 2005 - 12:15:01 CST)
  • Re: AMBER: troubleshooting replica exchange (Thu Oct 13 2005 - 02:44:59 CDT)
  • Re: AMBER: parallel error (Fri Jul 01 2005 - 10:51:18 CDT)
  • Re: AMBER: DNA base-flipping: TI vs PMF (Thu Jun 02 2005 - 12:21:56 CDT)
  • AMBER: write format of restart crd in sander/pmemd (Thu May 19 2005 - 07:12:22 CDT)
  • Re: AMBER: GB with Langevin dynamics - solution (Tue Apr 12 2005 - 12:39:54 CDT)
  • AMBER: GB with Langevin dynamics - solution (Mon Apr 11 2005 - 12:18:13 CDT)
  • AMBER: GB with Langevin dynamics problem 2 (Fri Apr 08 2005 - 11:29:08 CDT)
  • AMBER: GB with Langevin dynamics problem (Tue Apr 05 2005 - 11:04:15 CDT)
  • Re: AMBER: pmemd + pgi 5.1 + ntr = 1 (Thu Feb 24 2005 - 16:59:16 CST)
  • AMBER: pmemd + pgi 5.1 + ntr = 1 (Thu Feb 24 2005 - 16:25:04 CST)
• Petr Kulhanek
  • Re: AMBER: Ptraj and order of operations (Wed Jul 13 2005 - 02:21:48 CDT)
  • Re: AMBER: pmemd - bug report (Tue Jul 05 2005 - 11:29:54 CDT)
  • Re: AMBER: pmemd - bug report (Tue Jul 05 2005 - 05:31:14 CDT)
  • AMBER: pmemd - bug report (Mon Jul 04 2005 - 11:33:05 CDT)
  • Re: AMBER: nonbond_list question . (Sun Jun 19 2005 - 05:06:31 CDT)
  • Re: AMBER: Error on restrained MD equilibration (AMBER 7) (Wed Jun 01 2005 - 06:03:21 CDT)
  • Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? (Thu May 26 2005 - 05:44:37 CDT)
  • Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? (Wed May 25 2005 - 06:56:34 CDT)
  • Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth (Thu Apr 28 2005 - 02:02:47 CDT)
• Philippe ARNAUD
  • AMBER: PARMSCAN program (Wed May 25 2005 - 02:28:31 CDT)
• Phineus Markwick
  • AMBER: re: about run time in GB and PB (Thu Apr 21 2005 - 09:29:33 CDT)
  • Re: AMBER: about run time in GB and PB (Thu Apr 21 2005 - 09:10:20 CDT)
  • Re: AMBER: about run time in GB and PB (Thu Apr 21 2005 - 05:15:57 CDT)
  • Re: AMBER: about run time in GB and PB (Thu Apr 21 2005 - 03:26:26 CDT)
  • AMBER: ff02EP + pol3 (2) (Mon Apr 04 2005 - 07:06:36 CDT)
  • AMBER: problem with input files when using ff02EP + pol3 (Sun Apr 03 2005 - 07:35:28 CDT)
  • AMBER: scaleCharges with polarisable force fields (Fri Apr 01 2005 - 06:57:43 CST)
  • AMBER: TMD force constant (Tue Mar 22 2005 - 07:14:53 CST)
  • AMBER: lmanal input file problem (Fri Mar 18 2005 - 10:00:18 CST)
  • AMBER: problem with nmode using ntrun=5 (2) (Fri Mar 11 2005 - 10:39:43 CST)
  • AMBER: problem with nmode using ntrun=5 (Fri Mar 11 2005 - 08:38:34 CST)
• Piero Altoè
  • AMBER: restraintmask dimension (Wed Mar 16 2005 - 05:42:12 CST)
• Pieter Smith
  • AMBER: Problems Binding Protein to DNA (Tue Mar 08 2005 - 23:21:30 CST)
• ping jiang
  • Re: AMBER: problem of calculate the charge (Fri Dec 30 2005 - 12:48:41 CST)
  • AMBER: problem of calculate the charge2 (Tue Dec 27 2005 - 20:17:05 CST)
  • AMBER: problem of calculate the charge (Tue Dec 27 2005 - 18:47:16 CST)
  • Re: AMBER: (no subject) (Fri Dec 23 2005 - 20:25:19 CST)
  • AMBER: (no subject) (Fri Dec 23 2005 - 14:46:58 CST)
  • AMBER: To post or mail to the list (subscribers only) (Fri Dec 23 2005 - 14:07:45 CST)
• Ping Lin
  • AMBER: QM/MM with pmemd (Tue Jan 11 2005 - 13:08:45 CST)
• Piotr Cieplak
  • Re: AMBER: RESP: Question (Mon Dec 05 2005 - 12:00:37 CST)
  • Re: AMBER: PARM-99 (Fri Nov 25 2005 - 19:46:31 CST)
  • Re: AMBER: D-enantiomers (Thu Sep 22 2005 - 12:41:24 CDT)
  • Re: AMBER: D-enantiomers (Wed Sep 21 2005 - 03:13:26 CDT)
  • Re: AMBER: mm-pbsa with multiple-processors (Mon Mar 21 2005 - 18:17:30 CST)
  • Re: AMBER: R.E.D (Sun Mar 06 2005 - 18:20:42 CST)
  • Re: AMBER: problems with running sander in parallel on linux (Tue Feb 15 2005 - 15:58:09 CST)
  • Re: AMBER: problems with running sander in parallel on linux (Tue Feb 15 2005 - 14:55:59 CST)
  • RE: AMBER: problems with running sander in parallel on linux (Tue Feb 15 2005 - 13:01:15 CST)
  • AMBER: problems with running sander in parallel on linux (Tue Feb 15 2005 - 12:28:02 CST)
  • Re: AMBER: Scaling of charges in a polarizable simulation ! (Thu Jan 20 2005 - 00:56:04 CST)
  • Re: AMBER: Scaling of charges in a polarizable simulation ! (Wed Jan 19 2005 - 12:14:05 CST)
  • Re: AMBER: Steered Molecular Dynamics with AMBER? (Wed Jan 05 2005 - 01:29:41 CST)
• pl
  • Re: AMBER: problem with position restraints (refc file) (Wed Jan 19 2005 - 05:47:18 CST)
  • Re: AMBER: problem with position restraints (refc file) (Tue Jan 18 2005 - 11:13:17 CST)
  • AMBER: problem with position restraints (refc file) (Tue Jan 18 2005 - 09:25:27 CST)
  • Re: AMBER: Weighting of different restraint types? (Mon Jan 10 2005 - 03:27:19 CST)
  • AMBER: Weighting of different restraint types? (Fri Jan 07 2005 - 07:03:15 CST)
  • Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied (Tue Jan 04 2005 - 07:25:39 CST)
  • Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied (Tue Jan 04 2005 - 05:27:07 CST)
  • AMBER: Hbonds restraints OK but Dihedral restraints not applied (Mon Jan 03 2005 - 08:06:48 CST)
• pmullins
  • AMBER: Amber Installation (Fri Apr 22 2005 - 13:28:34 CDT)
• Pradipta Bandyopadhyay
  • AMBER: Problem with sander test suites in solaris ! (Fri Dec 02 2005 - 08:26:05 CST)
  • AMBER: Problem in running AMBER 7 in solaris ! (Fri Dec 02 2005 - 03:17:19 CST)
  • AMBER: addition to the last mail (lahey F95) ! (Mon Nov 07 2005 - 04:20:06 CST)
  • AMBER: AMBER 8 compilation with lahey F95 ! (Mon Nov 07 2005 - 04:13:57 CST)
  • AMBER: Energy output problem! (Tue Oct 04 2005 - 07:08:04 CDT)
  • AMBER: mm_pbsa script ! (Mon Jun 27 2005 - 01:43:53 CDT)
  • AMBER: MM_PBSA ! (Sun Jun 26 2005 - 07:43:18 CDT)
  • AMBER: GB with dipoles ! (Tue May 03 2005 - 06:54:44 CDT)
  • Re: AMBER: how to excite a single residue ? (Wed Mar 09 2005 - 23:24:34 CST)
  • AMBER: Compilation problem at dual processor linux ! (Wed Feb 02 2005 - 06:32:52 CST)
  • Re: AMBER: Scaling of charges in a polarizable simulation ! (Wed Jan 19 2005 - 22:54:13 CST)
  • AMBER: Scaling of charges in a polarizable simulation ! (Wed Jan 19 2005 - 10:02:37 CST)
• Pratul K. Agarwal
  • AMBER: Failed sander runs for large systems (Fri Jul 29 2005 - 21:41:44 CDT)
• Praveena Gopal
  • AMBER: AMBER-process_mdout.perl (Mon Jul 18 2005 - 02:26:19 CDT)
  • AMBER: Amber PBMD:Energy fluctuation (Sat Mar 12 2005 - 03:48:03 CST)
• praveena moldy
  • AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem (Sun Feb 27 2005 - 23:36:36 CST)
  • AMBER: Error while running resp. (Tue Jan 25 2005 - 08:28:55 CST)
  • AMBER: Error while running resp. (Tue Jan 25 2005 - 08:24:01 CST)
• Priti Hansia
  • Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN (Wed Dec 28 2005 - 07:05:56 CST)
  • Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN (Tue Dec 27 2005 - 11:35:41 CST)
  • AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN (Fri Dec 23 2005 - 05:28:57 CST)
  • AMBER: Radial Distribution functions by ptraj (Thu Dec 01 2005 - 13:44:02 CST)
  • AMBER: carnal problem (Thu Sep 08 2005 - 04:25:53 CDT)
  • AMBER: Error in minimization (Fri May 20 2005 - 05:58:36 CDT)
  • AMBER: how to excite a single residue ? (Wed Mar 09 2005 - 22:28:24 CST)
  • AMBER: (Wed Mar 09 2005 - 01:38:59 CST)
• protege_at_snu.ac.kr
  • Re: AMBER: spherical boundary condition (Mon Mar 14 2005 - 11:43:14 CST)
  • Re: AMBER: spherical boundary condition (Mon Mar 14 2005 - 11:43:14 CST)
• putra abdullah
  • AMBER: amber with mpich-G2 (Sun Mar 06 2005 - 20:55:44 CST)
• Qing Zhang
  • Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends (Tue Jul 12 2005 - 14:59:01 CDT)
  • Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends (Thu Jul 07 2005 - 19:48:40 CDT)
  • Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends (Thu Jul 07 2005 - 03:30:14 CDT)
• Qizhi Cui
  • AMBER: atom type for -CH=CH- (Thu Jun 09 2005 - 20:46:13 CDT)
• qlu_at_notes.cc.sunysb.edu
  • AMBER: Can REM be used as multiple normal sander jobs on parallel machine (Wed Feb 09 2005 - 17:15:59 CST)
• quch 2004
  • AMBER: strange case (Wed Sep 14 2005 - 16:57:28 CDT)
• Rachel Burdge
  • AMBER: anal and periodic boundary conditions (Wed Nov 16 2005 - 10:18:34 CST)
  • AMBER: AMBER on g5 10.4 w/g95 or gfortran (Tue Aug 16 2005 - 10:12:40 CDT)
  • Re: AMBER: sander errors with atom restraints on ia64 (Fri Feb 18 2005 - 10:04:17 CST)
  • AMBER: sander errors with atom restraints on ia64 (Thu Feb 17 2005 - 15:46:04 CST)
  • Re: AMBER: Poisson Boltzmann dynamics error (Thu Feb 10 2005 - 12:51:05 CST)
  • AMBER: Poisson Boltzmann dynamics error (Thu Feb 10 2005 - 10:04:55 CST)
• RadhaKumari Yadav
  • AMBER: Alignment tensor and Interia tensor (Sat Dec 03 2005 - 10:58:01 CST)
  • AMBER: Residual Dipolar Refinement (Wed Nov 30 2005 - 11:16:23 CST)
• Rajeev Ranjan Singh
  • Re: AMBER: error during MD run (Wed May 18 2005 - 13:16:12 CDT)
  • Re: AMBER: loading pdb (Wed May 18 2005 - 09:01:34 CDT)
  • AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN (Tue May 17 2005 - 15:15:33 CDT)
• Raviprasad Aduri
  • Re: AMBER: Modified RNA Bases (Tue Sep 27 2005 - 12:22:45 CDT)
  • AMBER: Modified RNA Bases (Mon Sep 26 2005 - 21:41:12 CDT)
  • Re: AMBER: RED and Multi-Orientation (Tue Sep 06 2005 - 20:24:29 CDT)
  • AMBER: RED and Multi-Orientation (Mon Sep 05 2005 - 21:34:56 CDT)
  • AMBER: Re:Antechamber (Tue Aug 30 2005 - 18:34:33 CDT)
  • AMBER: RED II and Gaussian (Wed Aug 24 2005 - 21:01:46 CDT)
• Ray Luo
  • Re: AMBER: question about mmpbsa (Thu Dec 15 2005 - 12:08:55 CST)
  • Re: AMBER: question about mmpbsa (Mon Dec 12 2005 - 21:34:13 CST)
  • Re: AMBER: The error during calculating PB with pbsa (Sun Dec 04 2005 - 20:16:09 CST)
  • Re: AMBER: Mg2+ issues of using MM-PB/GBSA (Wed Nov 30 2005 - 22:31:29 CST)
  • Re: AMBER: Mg2+ issues of using MM-PB/GBSA (Wed Nov 30 2005 - 20:04:55 CST)
  • Re: AMBER: Questions about MM-PBSA in Amber8 (Wed Nov 30 2005 - 18:39:50 CST)
  • Re: AMBER: Mg2+ issues of using MM-PB/GBSA (Wed Nov 30 2005 - 10:46:56 CST)
  • Re: AMBER: MM_PBSA stopped at some snapshot (Tue Nov 29 2005 - 20:55:41 CST)
  • Re: AMBER: MM_PBSA stopped at some snapshot (Sun Nov 27 2005 - 20:37:12 CST)
  • Re: AMBER: MM_PBSA_parameter (Wed Nov 23 2005 - 17:23:33 CST)
  • Re: AMBER: MM_PBSA_parameter (Wed Nov 23 2005 - 15:48:17 CST)
  • Re: AMBER: mm_pbsa (Sat Nov 12 2005 - 02:09:13 CST)
  • Re: AMBER: mm_pbsa (Fri Nov 11 2005 - 17:57:04 CST)
  • Re: AMBER: mm_pbsa (Tue Nov 08 2005 - 23:26:52 CST)
  • Re: AMBER: How is the origin of the grid defined?(PBSA question) (Mon Aug 22 2005 - 20:15:48 CDT)
  • Re: AMBER: mm_pbsa (Sun Aug 21 2005 - 13:29:41 CDT)
  • Re: AMBER: mm_pbsa (Thu Aug 18 2005 - 16:43:51 CDT)
  • Re: AMBER: How is the origin of the grid defined?(PBSA question) (Tue Aug 16 2005 - 08:46:01 CDT)
  • Re: AMBER: How is the origin of the grid defined?(PBSA question) (Sat Aug 13 2005 - 14:40:54 CDT)
  • Re: AMBER: Solute-solvent boundary in pbsa (Wed May 25 2005 - 20:40:39 CDT)
  • Re: AMBER: Solute-solvent boundary in pbsa (Wed May 25 2005 - 00:54:50 CDT)
  • Re: Re#2:Re: AMBER: Solute-solvent boundary in pbsa (Wed May 25 2005 - 00:56:08 CDT)
  • Re: AMBER: Solute-solvent boundary in pbsa (Tue May 24 2005 - 03:48:10 CDT)
  • Re: AMBER: error in pbsa calculation (Wed Apr 27 2005 - 12:03:33 CDT)
  • Re: AMBER: error in pbsa calculation (Tue Apr 26 2005 - 16:39:50 CDT)
  • Re: AMBER: strange VDWAALS and EEL energies calculated by pbsa (Thu Apr 21 2005 - 07:18:17 CDT)
  • Re: AMBER: solvent accessible surface area (Mon Apr 18 2005 - 21:12:54 CDT)
  • Re: AMBER: linit in mm-pbsa (Thu Apr 07 2005 - 23:30:06 CDT)
  • Re: AMBER: igb10 vlimit exceeded (Thu Mar 31 2005 - 10:52:50 CST)
  • Re: AMBER: warning in PBSA (Wed Mar 23 2005 - 11:42:34 CST)
  • Re: AMBER: igb=10 some vdW terms disappear? (Tue Mar 22 2005 - 16:59:00 CST)
  • Re: AMBER: igb=10 some vdW terms disappear? (Tue Mar 22 2005 - 15:54:57 CST)
  • Re: AMBER: igb=10 some vdW terms disappear? (Mon Mar 21 2005 - 11:15:24 CST)
  • Re: AMBER: "personality" of Amber force field (Thu Mar 17 2005 - 16:17:03 CST)
  • Re: AMBER: Poisson Boltzmann dynamics error (Tue Feb 08 2005 - 06:13:58 CST)
  • Re: AMBER: MM_PBSA fillratio error (Mon Jan 03 2005 - 16:28:46 CST)
• ReichertD_at_mir.wustl.edu
  • AMBER: problem with solvateBox (Fri Feb 25 2005 - 14:38:51 CST)
• René Ranzinger
  • AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_' (Tue May 24 2005 - 10:04:42 CDT)
• Rhoad, Jonathan S.
  • AMBER: ERROR in readParm: ...failed to find BONDS_WITHOUT_HYDROGEN (Fri Dec 02 2005 - 17:02:36 CST)
  • RE: AMBER: vdw of h atoms (Fri Oct 28 2005 - 18:56:24 CDT)
  • RE: AMBER: Leap set head/tail question (Tue Aug 02 2005 - 13:10:42 CDT)
  • RE: AMBER: pdb files from traj file (Wed Jul 13 2005 - 16:22:56 CDT)
  • RE: AMBER: TI - frcmod file (Wed Jul 13 2005 - 16:03:17 CDT)
  • RE: AMBER: Searching for NAD parameter files / Problems with parameter file creation (Thu Jun 23 2005 - 10:08:01 CDT)
  • RE: AMBER: vdw for terminal phosphate (Mon Jun 13 2005 - 11:21:49 CDT)
  • AMBER: vdw for terminal phosphate (Fri Jun 10 2005 - 11:16:47 CDT)
  • AMBER: RESP of negatively charged molecule (Tue Mar 01 2005 - 15:39:05 CST)
• riccardo nifosi
  • AMBER: quadrupole in resp (Wed May 25 2005 - 05:44:20 CDT)
• Rino Ragno
  • AMBER: AMBER8: compiling under cygwin using lahey fortran (Wed Jan 19 2005 - 16:13:07 CST)
  • AMBER: Steered Molecular Dynamics with AMBER? (Tue Jan 04 2005 - 16:33:09 CST)
• rluo_at_uci.edu
  • AMBER: (Sun Nov 06 2005 - 18:42:30 CST)
• Robert Duke
  • Re: AMBER: | ERROR: Could not read coords from rst file (Thu Dec 15 2005 - 21:14:35 CST)
  • Re: AMBER: parallel AMBER on cluster (Thu Dec 15 2005 - 12:37:22 CST)
  • Re: AMBER: Build for single precision (Thu Dec 15 2005 - 10:23:49 CST)
  • Re: AMBER: PMEMD limitation on NFFT (Fri Nov 04 2005 - 21:29:17 CST)
  • Re: AMBER: compiling amber with pgi 5.2.4 (Mon Oct 24 2005 - 07:44:42 CDT)
  • Re: AMBER: sander error (Tue Oct 18 2005 - 10:18:05 CDT)
  • Re: AMBER: sander error (Tue Oct 18 2005 - 09:49:05 CDT)
  • Re: AMBER: AMBER goes in a Loop (Fri Oct 14 2005 - 12:58:50 CDT)
  • Re: AMBER: amber8 parallel sander (Tue Oct 04 2005 - 00:26:28 CDT)
  • Re: AMBER: Amber compilation on opteron with PGI compiler (Fri Sep 30 2005 - 08:53:58 CDT)
  • Re: AMBER: amber8 parallel sander (Thu Sep 22 2005 - 16:47:10 CDT)
  • Re: AMBER: amber8 parallel sander (Thu Sep 22 2005 - 11:57:53 CDT)
  • Re: AMBER: Interpreting Amber8 Benchmark Results (Wed Aug 31 2005 - 16:37:53 CDT)
  • Re: AMBER: Interpreting Amber8 Benchmark Results (Wed Aug 31 2005 - 15:34:42 CDT)
  • AMBER: Critical PMEMD 8 Bugfix (Mon Jul 11 2005 - 07:38:59 CDT)
  • Re: AMBER: pmemd - bug report (Tue Jul 05 2005 - 11:47:19 CDT)
  • Re: AMBER: pmemd - bug report (Mon Jul 04 2005 - 22:58:14 CDT)
  • Re: AMBER: pmemd - bug report (Mon Jul 04 2005 - 16:40:18 CDT)
  • Re: AMBER: pmemd - bug report (Mon Jul 04 2005 - 15:30:54 CDT)
  • Re: AMBER: nonbond_list question . (Sun Jun 19 2005 - 09:25:37 CDT)
  • Re: AMBER: nonbond_list question . (Sat Jun 18 2005 - 22:03:07 CDT)
  • Re: AMBER: nmropt =1 AND ntr=1 in pmemd (Fri Jun 17 2005 - 16:58:44 CDT)
  • Re: AMBER: nmropt =1 AND ntr=1 in pmemd (Tue Jun 14 2005 - 07:18:20 CDT)
  • Re: AMBER: precision switch from 64 to 32 bit (double from single precision) (Thu Jun 09 2005 - 07:20:52 CDT)
  • Re: AMBER: Compile question?? (Mon Jun 06 2005 - 09:32:06 CDT)
  • Re: AMBER: Compile question?? (Mon Jun 06 2005 - 09:17:48 CDT)
  • Re: AMBER: Compile question?? (Mon Jun 06 2005 - 07:38:02 CDT)
  • Re: AMBER: setting up Parallel processing (Thu May 26 2005 - 11:15:30 CDT)
  • AMBER: Fw: Installing PMEMD on IBM machine (CPU power4) running SUSE_9.1 (Tue May 24 2005 - 09:42:15 CDT)
  • Re: AMBER: Amber 8 and LAM compilation problem (Thu May 19 2005 - 07:05:48 CDT)
  • Re: AMBER: compiling pmemd on dual xeon (Tue May 17 2005 - 12:49:48 CDT)
  • Re: AMBER: SANDER BOMB: volume of ucell too big (Thu May 12 2005 - 15:44:11 CDT)
  • Re: AMBER: AMBER8 Build on Linux x64 running Opterons (Wed May 11 2005 - 10:18:12 CDT)
  • Re: AMBER: AMBER8 Build on Linux x64 running Opterons (Wed May 11 2005 - 10:14:50 CDT)
  • Re: AMBER: doesn't work in pmemd, and no output in parallel simulations (Wed Apr 27 2005 - 07:06:46 CDT)
  • Re: AMBER: doesn't work in pmemd, and no output in parallel simulations (Tue Apr 26 2005 - 16:24:04 CDT)
  • Re: AMBER: Compiling on dual-opteron with pathscale 2.1 on RHEL 4 AS (Sat Apr 02 2005 - 18:42:47 CST)
  • Re: AMBER: PMEMD with big systems (Fri Mar 18 2005 - 18:12:24 CST)
  • Re: AMBER: compiler for amber8 on opteron (Fri Mar 18 2005 - 07:11:22 CST)
  • Re: AMBER: Sander questions on dual-processor Sun with MPICH (Wed Mar 09 2005 - 07:41:08 CST)
  • Re: AMBER: amber on sgi (Wed Mar 09 2005 - 07:32:29 CST)
  • AMBER: New pmemd build utility; pathscale vs. pgi vs. ifort em64 opteron benchmarks (Mon Mar 07 2005 - 10:47:02 CST)
  • Re: AMBER: amber with mpich-G2 (Sun Mar 06 2005 - 22:07:21 CST)
  • AMBER: PMEMD on Opterons; building/benchmarks/recommendations (Tue Mar 01 2005 - 13:14:56 CST)
  • AMBER: My last posting (Thu Feb 24 2005 - 22:15:08 CST)
  • Re: AMBER: parallel AMBER/pmemd installation problem on Opteron (Thu Feb 24 2005 - 22:06:54 CST)
  • Re: AMBER: pmemd + pgi 5.1 + ntr = 1 (Thu Feb 24 2005 - 17:22:37 CST)
  • Re: AMBER: pmemd + pgi 5.1 + ntr = 1 (Thu Feb 24 2005 - 16:38:02 CST)
  • Re: AMBER: RE:Amber 8 with lam compilation problem (Thu Feb 24 2005 - 07:54:08 CST)
  • Re: AMBER: parallel AMBER/pmemd installation problem on Opteron (Wed Feb 23 2005 - 11:27:13 CST)
  • Re: AMBER: parallel AMBER/pmemd installation problem on Opteron (Wed Feb 23 2005 - 07:17:54 CST)
  • Re: AMBER: problem with protein minimization (Tue Feb 22 2005 - 11:10:51 CST)
  • AMBER: Re: pmemd problems (Thu Feb 17 2005 - 09:15:33 CST)
  • Re: AMBER: Amber7 nmropt (Wed Feb 16 2005 - 17:05:37 CST)
  • Re: AMBER: problems with running sander in parallel on linux (Tue Feb 15 2005 - 15:25:52 CST)
  • Re: AMBER: problems with running sander in parallel on linux (Tue Feb 15 2005 - 13:43:37 CST)
  • Re: AMBER: pmemd and restraints (Thu Jan 27 2005 - 07:15:00 CST)
  • Re: AMBER: pmemd and restraints (Wed Jan 26 2005 - 11:45:01 CST)
  • Re: AMBER: amber 8 benchmarks dec alpha (Mon Jan 24 2005 - 16:27:50 CST)
  • Re: AMBER: amber 8 installation (Fri Jan 21 2005 - 12:03:42 CST)
  • Re: AMBER: pmemd and distance restraint (Thu Jan 20 2005 - 21:12:17 CST)
  • Re: AMBER: pmemd and distance restraint (Thu Jan 20 2005 - 06:41:30 CST)
  • Re: AMBER: amber8 parallel sander (Mon Jan 17 2005 - 12:13:10 CST)
  • Re: AMBER: distance restraint and file fort.35 (Mon Jan 17 2005 - 08:48:57 CST)
  • Re: AMBER: amber8 parallel sander (Wed Jan 12 2005 - 09:20:40 CST)
  • Re: AMBER: amber8 parallel sander (Wed Jan 12 2005 - 07:03:05 CST)
  • Re: AMBER: Floating Exception and installation on Digital Unix. (Tue Jan 11 2005 - 07:18:20 CST)
  • Re: AMBER: Floating Exception and installation on Digital Unix. (Sun Jan 09 2005 - 11:54:16 CST)
  • Re: AMBER: Floating Exception in sander (Fri Jan 07 2005 - 07:15:44 CST)
  • Re: AMBER: Floating Exception in sander (Wed Jan 05 2005 - 07:55:22 CST)
• Robert J. Woods
  • Re: AMBER: Amber Performance in Parallel on Itanium (Wed Mar 30 2005 - 10:47:25 CST)
  • AMBER: Amber Performance in Parallel on Itanium (Wed Mar 30 2005 - 09:32:10 CST)
• Roberto Gomperts
  • Re: AMBER: Strange difference in speed between Altix (Itanium2) and Tezro (MIPS) SGI for small GB/SA run (Thu Aug 04 2005 - 06:57:12 CDT)
  • Re: AMBER: error - compiling antechamber (Wed Jun 29 2005 - 16:11:41 CDT)
  • Re: [pgannett@hsc.wvu.edu: AMBER: compiler error, SGI Octane] (Wed Jun 29 2005 - 10:01:00 CDT)
• Rogelio Adams
  • 75% Off for All New Softs Now! haberman (Fri May 06 2005 - 22:19:57 CDT)
• Ross Walker
  • RE: AMBER: non bond over flow (Thu Dec 29 2005 - 10:15:35 CST)
  • RE: AMBER: parallel AMBER on cluster (Thu Dec 15 2005 - 12:38:57 CST)
  • RE: AMBER: Build for single precision (Thu Dec 15 2005 - 10:29:35 CST)
  • RE: AMBER: E of amber calculations (Thu Dec 15 2005 - 10:23:46 CST)
  • RE: AMBER: error with compiling amber8 with lam on intel pc clusters (Thu Dec 15 2005 - 10:11:05 CST)
  • RE: Re[2]: AMBER: What does a crash mean while running a md simulation? (Tue Dec 06 2005 - 10:54:11 CST)
  • RE: Re[2]: AMBER: AMBER compilation with -DREM (Wed Nov 30 2005 - 10:26:29 CST)
  • RE: AMBER: question convert crd files to pdb files (Tue Nov 29 2005 - 22:27:02 CST)
  • RE: AMBER: constant pressure vs. constant volume heating (Tue Nov 29 2005 - 13:20:38 CST)
  • RE: AMBER: cluster analysis (Wed Nov 23 2005 - 10:15:53 CST)
  • RE: AMBER: Leap handling crystallographic waters (Tue Nov 22 2005 - 14:09:27 CST)
  • RE: AMBER: Leap handling crystallographic waters (Tue Nov 22 2005 - 11:46:38 CST)
  • RE: AMBER: How to use XLEAP to link one atom in a monomer to another atom in another monomer? (where both the 2 monomers are in a same pdb file) (Mon Nov 21 2005 - 10:33:44 CST)
  • RE: AMBER: average struct without solvent (Mon Nov 21 2005 - 10:28:23 CST)
  • RE: AMBER: How to use XLEAP to link one atom in a monomer to another atom in another monomer? (where both the 2 monomers are in a same pdb file) (Sun Nov 20 2005 - 23:59:18 CST)
  • RE: AMBER: Question about PDB format (Sat Nov 19 2005 - 10:55:11 CST)
  • RE: AMBER: need clarification on EWALD BOMB error (Thu Nov 17 2005 - 10:20:02 CST)
  • RE: AMBER: ew_legal.h (Mon Nov 14 2005 - 21:22:31 CST)
  • RE: AMBER: Error message (Mon Nov 14 2005 - 09:04:04 CST)
  • RE: AMBER: Making movie from AMBER trajectory (Mon Nov 07 2005 - 10:55:48 CST)
  • RE: AMBER: restart file and crd file (Fri Nov 04 2005 - 10:22:41 CST)
  • RE: AMBER: EEL and EAMBER values (Wed Nov 02 2005 - 23:02:44 CST)
  • RE: AMBER: Density of Cyclohexane box (Wed Nov 02 2005 - 22:52:32 CST)
  • RE: AMBER: Improper Torsional Parameters (Wed Nov 02 2005 - 22:06:28 CST)
  • RE: AMBER: fedora installation problem (Wed Nov 02 2005 - 10:50:03 CST)
  • RE: AMBER: error in safe (Mon Oct 24 2005 - 09:25:38 CDT)
  • RE: AMBER: Problem with the QMMM example in AMBER 2004 tutorial (Sun Oct 23 2005 - 12:02:55 CDT)
  • RE: AMBER: xleap with modified residue (Thu Oct 20 2005 - 13:58:53 CDT)
  • RE: AMBER: antechamber -- missing improper torsions (Tue Oct 18 2005 - 22:33:13 CDT)
  • RE: AMBER: sander error (Tue Oct 18 2005 - 09:23:18 CDT)
  • RE: AMBER: antechamber -- missing improper torsions (Mon Oct 17 2005 - 17:04:23 CDT)
  • RE: AMBER: Cyclohexane solvent Box (Mon Oct 17 2005 - 09:03:54 CDT)
  • RE: AMBER: Scaling factor of NMR restraint (Fri Oct 14 2005 - 09:55:44 CDT)
  • RE: AMBER: QMMM question (Mon Oct 10 2005 - 09:38:50 CDT)
  • RE: AMBER: sander error (Mon Oct 10 2005 - 09:13:35 CDT)
  • RE: AMBER: question temperature coupling tautp value for RNA (Mon Oct 03 2005 - 17:50:47 CDT)
  • RE: AMBER: Problem during Production (Sat Sep 24 2005 - 10:54:38 CDT)
  • RE: AMBER: Could not open file (Melb.mdcrd) with mode (r) (Tue Sep 20 2005 - 16:39:20 CDT)
  • RE: AMBER: Xleap menu bar problems (Mon Sep 19 2005 - 14:44:11 CDT)
  • RE: AMBER: Could not open file (Melb.mdcrd) with mode (r) (Mon Sep 19 2005 - 12:17:29 CDT)
  • RE: AMBER: sander prob (Sat Sep 17 2005 - 11:23:27 CDT)
  • RE: AMBER: Problem with installation AMBER8 on Solaris 8 using original SUN compilers (Thu Sep 15 2005 - 19:36:49 CDT)
  • RE: AMBER: Problem with installation AMBER8 on Solaris 8 using original SUN compilers (Thu Sep 15 2005 - 15:48:38 CDT)
  • RE: AMBER: Problem with installation AMBER8 on Solaris 8 using original SUN compilers (Thu Sep 15 2005 - 12:05:36 CDT)
  • RE: AMBER: Error in "restrt" output file (Wed Sep 14 2005 - 16:46:40 CDT)
  • RE: AMBER: amber compilation on SGI ALTIX 350 (TEST FAILD) (Fri Sep 09 2005 - 12:37:30 CDT)
  • RE: AMBER: Amber 8 and PATH buffer overflow (Thu Sep 08 2005 - 12:26:52 CDT)
  • RE: AMBER: Amber 8 and PATH buffer overflow (Thu Sep 08 2005 - 12:22:23 CDT)
  • RE: AMBER: masks in ptraj - Hbond analysis (Tue Sep 06 2005 - 15:13:50 CDT)
  • RE: AMBER: unstable MD velocities (Thu Sep 01 2005 - 13:06:08 CDT)
  • RE: AMBER: Interpreting Amber8 Benchmark Results (Wed Aug 31 2005 - 16:00:55 CDT)
  • RE: AMBER: Interpreting Amber8 Benchmark Results (Wed Aug 31 2005 - 15:09:20 CDT)
  • RE: AMBER: disulfide bonds by "bond" or "edit -> draw" ? (Wed Aug 31 2005 - 11:48:39 CDT)
  • RE: AMBER: floating point exception (Wed Aug 31 2005 - 11:51:27 CDT)
  • RE: AMBER: params for cofactors (Mon Aug 29 2005 - 15:10:55 CDT)
  • RE: AMBER: Temperature equilibration (Mon Aug 29 2005 - 10:44:08 CDT)
  • RE: AMBER: Add constraints over time (Fri Aug 26 2005 - 11:41:04 CDT)
  • RE: AMBER: minimization (Fri Aug 26 2005 - 10:07:59 CDT)
  • RE: AMBER: ew_bspline.h error (Fri Aug 26 2005 - 10:03:29 CDT)
  • RE: AMBER: ptraj efficiency (Wed Aug 24 2005 - 13:29:36 CDT)
  • RE: AMBER: a problem encountered when trying to equalibrate alanine dipeptide in explicit water (Wed Aug 24 2005 - 12:45:59 CDT)
  • RE: AMBER: How to deal with the problem that a molecule go out the virtual box in vaccum (Tue Aug 23 2005 - 23:42:52 CDT)
  • RE: AMBER: minimization stuck problem (Tue Aug 23 2005 - 10:22:53 CDT)
  • RE: AMBER: minimization stuck problem (Sun Aug 21 2005 - 15:02:09 CDT)
  • RE: AMBER: minimization stuck problem (Sat Aug 20 2005 - 13:00:11 CDT)
  • RE: AMBER: min problem (Fri Aug 19 2005 - 13:52:36 CDT)
  • RE: AMBER: parallel amber8 with mpi through qsnet (Fri Aug 19 2005 - 13:42:40 CDT)
  • RE: AMBER: ew_bspline.h error (Fri Aug 19 2005 - 13:33:57 CDT)
  • RE: AMBER: QM/MM (Fri Aug 19 2005 - 13:27:44 CDT)
  • RE: AMBER: group-based cutoff (Wed Aug 10 2005 - 20:57:35 CDT)
  • RE: AMBER: Tutorial question and some more... (Tue Aug 09 2005 - 14:03:01 CDT)
  • RE: AMBER: Convert .prmtop (AMBER7/8) to old format (AMBER6) (Sat Aug 06 2005 - 13:47:26 CDT)
  • RE: AMBER: installing amber7 on 64bit cluster (Thu Aug 04 2005 - 01:39:22 CDT)
  • RE: AMBER: bond parameters (Wed Aug 03 2005 - 11:11:00 CDT)
  • RE: AMBER: bond breaking/ energetic ion (Tue Aug 02 2005 - 21:26:02 CDT)
  • RE: AMBER: Leap set head/tail question (Tue Aug 02 2005 - 13:28:03 CDT)
  • RE: AMBER: strange minimalization output (Tue Aug 02 2005 - 10:47:59 CDT)
  • RE: AMBER: memory_mm_pbsa (Mon Aug 01 2005 - 22:14:47 CDT)
  • RE: AMBER: AMBER8 limitation of memory in QM/MM calculation (Mon Aug 01 2005 - 21:52:32 CDT)
  • RE: AMBER: AMBER8 limitation of memory in QM/MM calculation (Mon Aug 01 2005 - 21:52:29 CDT)
  • RE: AMBER: coordinated water molecules deleted when addions (Mon Aug 01 2005 - 12:09:17 CDT)
  • RE: AMBER: new residue (Wed Jul 27 2005 - 11:54:14 CDT)
  • RE: AMBER: Periodic box imaging using ptraj (Wed Jul 27 2005 - 11:28:05 CDT)
  • RE: AMBER: Tutoial 8 (Case Study) (Tue Jul 26 2005 - 12:03:37 CDT)
  • RE: AMBER: Trouble with Amber8 (Tue Jul 19 2005 - 15:41:27 CDT)
  • RE: AMBER: pdb file and xleap (Tue Jul 19 2005 - 10:33:44 CDT)
  • RE: AMBER: Amber 7 Compiler Error (Tue Jul 19 2005 - 10:36:03 CDT)
  • RE: AMBER: AMBER-process_mdout.perl (Mon Jul 18 2005 - 10:24:18 CDT)
  • RE: AMBER: P4 EM64T Intel Fortran Compile Problem (Fri Jul 15 2005 - 12:26:36 CDT)
  • RE: AMBER: pdb files from traj file (Wed Jul 13 2005 - 16:37:05 CDT)
  • RE: AMBER: MD simulation on a protein solvated by a combination of some water models ? (Tue Jul 12 2005 - 11:41:44 CDT)
  • RE: AMBER: Leap compilation issues (Tue Jul 12 2005 - 11:47:05 CDT)
  • RE: AMBER: Leap compilation issues (Mon Jul 11 2005 - 12:05:25 CDT)
  • RE: AMBER: molecular dynamics (Sat Jul 09 2005 - 22:42:06 CDT)
  • RE: AMBER: sander problem (Wed Jul 06 2005 - 16:19:34 CDT)
  • RE: AMBER: restart file (Tue Jul 05 2005 - 16:15:49 CDT)
  • RE: AMBER: restart file (Tue Jul 05 2005 - 14:29:27 CDT)
  • RE: AMBER: Loading a macmodel file complex (Tue Jul 05 2005 - 10:54:57 CDT)
  • RE: AMBER: Problems with parameter lib and prep püarameter files (Tue Jul 05 2005 - 10:47:22 CDT)
  • RE: AMBER: Is the MD simulation normal (Wed Jun 29 2005 - 11:09:13 CDT)
  • RE: AMBER: script for calculating hydrogen bond (Mon Jun 27 2005 - 22:04:43 CDT)
  • RE: AMBER: Searching for NAD parameter files / Problems with parameter file creation (Thu Jun 23 2005 - 11:26:56 CDT)
  • AMBER: RE: tutorial 8 (Wed Jun 22 2005 - 16:15:33 CDT)
  • RE: AMBER: How to turn off pme when using periodic box (Mon Jun 20 2005 - 15:31:04 CDT)
  • RE: AMBER: average structure (Sun Jun 19 2005 - 19:41:07 CDT)
  • AMBER: RE: AMBER :LINMIN problem (Fri Jun 17 2005 - 13:27:25 CDT)
  • RE: AMBER: Installation problem. . (Fri Jun 17 2005 - 12:39:15 CDT)
  • RE: AMBER: Installation problem. . (Fri Jun 17 2005 - 11:33:42 CDT)
  • RE: AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians (Thu Jun 16 2005 - 17:00:41 CDT)
  • RE: AMBER: How to modify force constants and equalibrium values for standard residues (Thu Jun 16 2005 - 16:05:33 CDT)
  • RE: AMBER: Installation problem. . (Wed Jun 15 2005 - 11:46:25 CDT)
  • RE: AMBER: solutions of amber installation problems (Tue Jun 14 2005 - 23:55:20 CDT)
  • RE: AMBER: creating pdb file.... (Tue Jun 14 2005 - 12:51:21 CDT)
  • RE: AMBER: compiler (Tue Jun 14 2005 - 12:43:58 CDT)
  • RE: AMBER: Extended bonds-MD (Tue Jun 14 2005 - 12:28:43 CDT)
  • RE: AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 22:49:05 CDT)
  • RE: AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 18:24:21 CDT)
  • RE: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 12:25:26 CDT)
  • RE: AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 12:19:04 CDT)
  • RE: AMBER: SHAKE in md with partial solvation (Mon Jun 06 2005 - 12:12:20 CDT)
  • RE: AMBER: New problem of parallel sander (Fri Jun 03 2005 - 11:53:55 CDT)
  • RE: AMBER: (Fri Jun 03 2005 - 11:51:48 CDT)
  • RE: AMBER: Build of AMBER for YDL ? (Wed Jun 01 2005 - 18:29:49 CDT)
  • RE: AMBER: problem in minimization (Wed Jun 01 2005 - 11:56:46 CDT)
  • RE: AMBER: density problem (Wed Jun 01 2005 - 11:21:33 CDT)
  • RE: AMBER: double counting of potentials (Tue May 31 2005 - 18:21:43 CDT)
  • RE: AMBER: meaningful tax for sander question (Tue May 31 2005 - 15:12:10 CDT)
  • RE: AMBER: meaningful tax for sander question (Tue May 31 2005 - 14:55:14 CDT)
  • RE: AMBER:Sander errors: Unit 6 Error on OPEN: mdout (Tue May 31 2005 - 12:45:53 CDT)
  • RE: AMBER: runtime error in sander? (Tue May 31 2005 - 12:34:51 CDT)
  • RE: AMBER: STOP 0 (Tue May 31 2005 - 11:47:20 CDT)
  • RE: AMBER: Error on restrained MD equilibration (AMBER 7) (Tue May 31 2005 - 11:45:19 CDT)
  • RE: AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" (Tue May 31 2005 - 11:09:20 CDT)
  • RE: AMBER: stack terminated abnormally (Tue May 31 2005 - 10:35:15 CDT)
  • RE: AMBER: density problem (Tue May 31 2005 - 10:33:39 CDT)
  • AMBER: Workshop Tutorials Downtime this weekend. (Fri May 27 2005 - 16:49:05 CDT)
  • RE: AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_' (Tue May 24 2005 - 10:43:37 CDT)
  • RE: AMBER: Error in sander: stack trace terminated abnormally. (Sun May 22 2005 - 16:53:36 CDT)
  • RE: AMBER: read pdb back to xleap after solvation of chloroform (Thu May 19 2005 - 20:41:31 CDT)
  • RE: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue (Thu May 19 2005 - 02:16:41 CDT)
  • RE: AMBER: Using AMBER for Carbon nanotubes (Wed May 18 2005 - 12:12:29 CDT)
  • AMBER: RE: Tutorial#1 ptraj/sander problem (Tue May 17 2005 - 17:56:59 CDT)
  • RE: AMBER: Tutorial #1 ptraj/sander problem (Thu May 12 2005 - 17:33:44 CDT)
  • RE: AMBER: Asking how to creat alanine "dipeptide" in amber8 (Wed May 11 2005 - 12:13:30 CDT)
  • RE: AMBER: problem with gb md (Thu May 05 2005 - 23:47:40 CDT)
  • RE: AMBER: serial and parallel (Sun Apr 24 2005 - 13:49:38 CDT)
  • RE: AMBER: Sander bomb - atom out of bounds (Thu Apr 21 2005 - 13:02:18 CDT)
  • RE: AMBER: intramolecular nonbonded interactions in AMBER force field (Wed Apr 20 2005 - 17:33:41 CDT)
  • AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation. (Wed Apr 20 2005 - 12:04:03 CDT)
  • RE: AMBER:Bond lengths aren't reasonable after minimisation. (Mon Apr 18 2005 - 11:55:54 CDT)
  • RE: AMBER: xleap, lib file question (Wed Apr 13 2005 - 17:07:04 CDT)
  • RE: AMBER: what is wrong with my amber job or installation? (Wed Apr 13 2005 - 15:46:01 CDT)
  • RE: AMBER: peptide side chain modification with LEAP (Tue Apr 12 2005 - 10:45:23 CDT)
  • RE: AMBER: A question on connecting residues in xleap (Mon Apr 11 2005 - 12:13:15 CDT)
  • RE: AMBER: A question on connecting residues in xleap (Mon Apr 11 2005 - 00:00:34 CDT)
  • RE: AMBER: A question on connecting residues in xleap (Sun Apr 10 2005 - 13:25:16 CDT)
  • AMBER: RE: system comparison for amber (Thu Apr 07 2005 - 11:41:06 CDT)
  • RE: AMBER: Amber Performance in Parallel on Itanium (Wed Mar 30 2005 - 10:20:14 CST)
  • RE: AMBER: tleap,xleap bond order for triple bonds (Tue Mar 29 2005 - 17:58:51 CST)
  • RE: AMBER: missing residue (Mon Mar 28 2005 - 10:23:47 CST)
  • RE: AMBER: Could not open file (trajin) with mode (r) (Wed Mar 23 2005 - 12:13:56 CST)
  • RE: AMBER: wierd behavior of addions (Tue Mar 22 2005 - 13:45:32 CST)
  • RE: AMBER: Amber8 Parallel installation troubles (Tue Mar 22 2005 - 13:20:22 CST)
  • RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem (Tue Mar 22 2005 - 12:05:15 CST)
  • RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem (Mon Mar 21 2005 - 18:54:52 CST)
  • RE: AMBER: Problem saving file in xleap (Tue Mar 15 2005 - 12:02:32 CST)
  • RE: AMBER: leap warnings (Mon Mar 14 2005 - 00:56:17 CST)
  • RE: AMBER: (Sun Mar 13 2005 - 18:29:08 CST)
  • RE: AMBER: The pressure (Tue Mar 08 2005 - 20:20:44 CST)
  • RE: AMBER: capping? (Tue Mar 08 2005 - 20:09:44 CST)
  • RE: AMBER: X Windows for LEaP on SGI (Tue Mar 08 2005 - 20:05:01 CST)
  • RE: AMBER: Sander questions on dual-processor Sun with MPICH (Tue Mar 08 2005 - 19:50:55 CST)
  • RE: AMBER: What PRESS is? (Mon Mar 07 2005 - 22:07:37 CST)
  • RE: AMBER: Dihedral Energy calculation (Wed Mar 02 2005 - 16:37:20 CST)
  • RE: AMBER: Dihedral Energy calculation (Wed Mar 02 2005 - 10:48:56 CST)
  • RE: AMBER: problem with MD simulation (Tue Mar 01 2005 - 10:51:40 CST)
  • RE: AMBER: NaNQ (Tue Mar 01 2005 - 10:46:08 CST)
  • RE: AMBER: Antechamber/formatting question (Sun Feb 27 2005 - 13:56:18 CST)
  • RE: AMBER: Pyranose pucker parameters (Sun Feb 27 2005 - 13:58:30 CST)
  • RE: AMBER: RE:Amber 8 with lam compilation problem (Wed Feb 23 2005 - 12:02:47 CST)
  • RE: AMBER: RE:Amber 8 with lam compilation problem (Wed Feb 23 2005 - 01:20:54 CST)
  • RE: AMBER: size of solventbox (Tue Feb 22 2005 - 23:22:03 CST)
  • RE: AMBER: Amber8 Solaris installation failure (Tue Feb 22 2005 - 17:55:17 CST)
  • RE: AMBER: MPI for sander8 (Tue Feb 22 2005 - 11:54:37 CST)
  • RE: AMBER: problem with protein minimization (Tue Feb 22 2005 - 10:47:56 CST)
  • RE: AMBER: Amber 8 with lam compilation problem (Mon Feb 21 2005 - 03:20:21 CST)
  • RE: AMBER: Amber: sander error segmentation fault. (Sat Feb 19 2005 - 00:34:22 CST)
  • RE: AMBER: DNA Tutorial (Fri Feb 18 2005 - 19:15:31 CST)
  • RE: AMBER: molecule blowing apart during equilibration (Fri Feb 18 2005 - 10:56:30 CST)
  • RE: AMBER: Amber7 nmropt (Wed Feb 16 2005 - 15:55:40 CST)
  • RE: AMBER: Amber7 nmropt (Wed Feb 16 2005 - 15:32:05 CST)
  • RE: AMBER: problems with running sander in parallel on linux (Tue Feb 15 2005 - 12:50:53 CST)
  • RE: AMBER: running shell scripts in tleap? (Mon Feb 14 2005 - 17:31:03 CST)
  • RE: AMBER: Restart Problem (Mon Feb 14 2005 - 14:01:16 CST)
  • RE: AMBER: vlimit (Mon Feb 14 2005 - 11:14:56 CST)
  • RE: AMBER: constrains (Mon Feb 14 2005 - 11:10:42 CST)
  • RE: AMBER: AMBER 8 : Water cap problem (Mon Feb 14 2005 - 11:07:21 CST)
  • RE: AMBER: (Mon Feb 14 2005 - 11:03:52 CST)
  • RE: AMBER: Poisson Boltzmann dynamics error (Thu Feb 10 2005 - 11:03:46 CST)
  • RE: AMBER: Convert to Pdb (Wed Feb 09 2005 - 13:19:15 CST)
  • RE: AMBER: tleap load pdb file (Wed Feb 09 2005 - 13:18:31 CST)
  • RE: AMBER: energy plot in minimization (Wed Feb 09 2005 - 12:10:13 CST)
  • RE: AMBER: Amber8 installation test possible failures (Tue Feb 08 2005 - 14:17:40 CST)
  • RE: AMBER: Linux Enterprise (Tue Feb 08 2005 - 13:59:43 CST)
  • RE: AMBER: tleap load pdb file (Sun Feb 06 2005 - 12:50:29 CST)
  • RE: AMBER: trajectory of minimization (Sun Feb 06 2005 - 12:36:29 CST)
  • RE: AMBER: non-periodic condition (Thu Feb 03 2005 - 12:27:30 CST)
  • RE: AMBER: sander segmentation fault (Wed Feb 02 2005 - 20:05:41 CST)
  • RE: AMBER: amber 8 system requirements (Wed Feb 02 2005 - 12:47:55 CST)
  • RE: AMBER: Compilation problem at dual processor linux ! (Wed Feb 02 2005 - 11:52:10 CST)
  • RE: AMBER: Problems with xLEaP (Fri Jan 28 2005 - 18:29:10 CST)
  • RE: AMBER: NCOPY definition (Fri Jan 28 2005 - 17:18:05 CST)
  • RE: AMBER: Problems with xLEaP (Fri Jan 28 2005 - 16:19:52 CST)
  • RE: AMBER: question about xwin load pdb file (Fri Jan 28 2005 - 12:20:18 CST)
  • RE: AMBER: &dipoles in sander (Fri Jan 28 2005 - 12:10:21 CST)
  • RE: AMBER: question about xwin load pdb file (Thu Jan 27 2005 - 23:38:30 CST)
  • RE: AMBER: problem with pressure equilibration (Thu Jan 27 2005 - 16:45:20 CST)
  • RE: AMBER: Increasing Volume with ntb=1 (Thu Jan 27 2005 - 12:13:27 CST)
  • RE: AMBER: Increasing Volume with ntb=1 (Wed Jan 26 2005 - 16:59:57 CST)
  • RE: AMBER: Increasing Volume with ntb=1 (Wed Jan 26 2005 - 14:42:13 CST)
  • RE: AMBER: how to solvate in TIP5P box (Wed Jan 26 2005 - 12:26:22 CST)
  • RE: AMBER: NAN errors (Tue Jan 25 2005 - 15:56:33 CST)
  • RE: AMBER: What does a crash mean while running a md simulation? (Tue Jan 25 2005 - 00:28:32 CST)
  • RE: AMBER: What does a crash mean while running a md simulation? (Mon Jan 24 2005 - 13:19:48 CST)
  • RE: AMBER: nmode calculation (Mon Jan 24 2005 - 13:13:59 CST)
  • RE: AMBER: &dipoles in sander (Sat Jan 22 2005 - 13:11:54 CST)
  • RE: AMBER: &dipoles in sander (Fri Jan 21 2005 - 12:26:24 CST)
  • RE: AMBER: Suspended (tty input) (Thu Jan 20 2005 - 17:58:13 CST)
  • RE: AMBER: sander failure (Thu Jan 20 2005 - 16:47:34 CST)
  • RE: AMBER: sander failure (Thu Jan 20 2005 - 16:26:58 CST)
  • RE: AMBER: sander failure (Thu Jan 20 2005 - 16:04:32 CST)
  • RE: AMBER: Can someone recommend a tutorial? (Thu Jan 20 2005 - 14:37:22 CST)
  • RE: AMBER: Compiling AMBER 8 for Mac OSX (Parallel) (Wed Jan 19 2005 - 12:23:40 CST)
  • RE: AMBER: new aminoacid (Mon Jan 17 2005 - 12:34:05 CST)
  • RE: AMBER: Coordinate Superimposition in PTRAJ (Sun Jan 16 2005 - 12:59:48 CST)
  • FW: AMBER: parametrization problem (Fri Jan 14 2005 - 16:39:12 CST)
  • RE: AMBER: AMBER tutorial ambpdb question (Mon Jan 10 2005 - 20:14:49 CST)
  • RE: AMBER: istart2 (Mon Jan 10 2005 - 11:18:32 CST)
  • RE: AMBER: Questions about sander.QMMM (Fri Jan 07 2005 - 13:38:29 CST)
• ross_at_rosswalker.co.uk
  • RE: AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? (Sat May 14 2005 - 14:43:46 CDT)
• rpaduri_at_chem.wayne.edu
  • Re: AMBER: Any way to get different charge on same type atom (Wed Nov 30 2005 - 18:37:13 CST)
  • Re: AMBER: RED II and Gaussian (Sat Aug 27 2005 - 17:40:53 CDT)
  • AMBER: PLease remove my post (Thu Aug 25 2005 - 11:08:38 CDT)
• Ru-Zhen Li
  • Re: AMBER: problem with running AMBER with lam-mpi though PBS script (Wed Mar 09 2005 - 19:48:56 CST)
  • AMBER: problem with running AMBER with lam-mpi though PBS script (Wed Mar 09 2005 - 08:01:24 CST)
• Russel Granger
  • A new rollax repliccas is in the mark. attitudinal (Sat May 14 2005 - 11:02:36 CDT)
• S. Frank Yan
  • Re: AMBER: mpirun sander8 problem (Thu Feb 24 2005 - 10:30:23 CST)
  • FW: AMBER: mpirun sander8 problem (Thu Feb 24 2005 - 02:41:14 CST)
  • RE: AMBER: mpirun sander8 problem (Wed Feb 23 2005 - 10:58:08 CST)
  • AMBER: mpirun sander8 problem (Wed Feb 23 2005 - 01:13:34 CST)
  • AMBER: MPI for sander8 (Tue Feb 22 2005 - 11:04:56 CST)
  • RE: AMBER: Linux Enterprise (Tue Feb 08 2005 - 13:45:40 CST)
  • RE: AMBER: Redhat Enterprise Linux (Tue Feb 01 2005 - 11:57:00 CST)
• S. Teletchéa
  • Re: AMBER: Solution for those who have mpich problem while building the parallel version of AMBER 8 (Wed Aug 17 2005 - 18:22:43 CDT)
• S.Sundar Raman
  • AMBER: non bond over flow (Wed Dec 28 2005 - 21:50:27 CST)
  • Re: AMBER: regarding ambpdb (Thu Dec 01 2005 - 07:39:31 CST)
  • AMBER: regarding ambpdb (Thu Dec 01 2005 - 04:40:58 CST)
  • Re: AMBER: need clarification on EWALD BOMB error (Thu Nov 17 2005 - 21:38:43 CST)
  • AMBER: need clarification on EWALD BOMB error (Thu Nov 17 2005 - 04:03:22 CST)
  • AMBER: ptraj hbond analysis (Wed Oct 19 2005 - 08:28:09 CDT)
  • AMBER: Free energy for L and D amino acids (Sun Oct 16 2005 - 10:40:24 CDT)
  • Re: AMBER: Quick question about xLeap (Thu Sep 08 2005 - 10:33:36 CDT)
  • Re: AMBER: (no subject) (Sat Jul 02 2005 - 07:58:59 CDT)
  • AMBER: Request for calculating free energy using AMBER6 (Mon Jun 27 2005 - 06:59:00 CDT)
  • AMBER: Need help in charge fitting through RESP (Mon Jun 13 2005 - 08:55:29 CDT)
  • AMBER: about equilibration dynamics (Mon Apr 18 2005 - 02:18:10 CDT)
  • AMBER: freee energy calculation without minimised structure (Wed Apr 13 2005 - 02:00:08 CDT)
  • AMBER: how to cap regions (Tue Mar 29 2005 - 23:00:12 CST)
  • AMBER: Minimization failure (Tue Mar 29 2005 - 22:47:22 CST)
  • AMBER: Installation problem (Thu Mar 03 2005 - 00:28:29 CST)
  • AMBER: Amber: sander error segmentation fault. (Sat Feb 19 2005 - 00:03:50 CST)
  • Re: AMBER:how to analyse trajectory files (Mon Feb 14 2005 - 22:58:19 CST)
  • AMBER:how to analyse trajectory files (Mon Feb 14 2005 - 03:17:39 CST)
  • AMBER: (Mon Feb 14 2005 - 03:03:27 CST)
  • Re: AMBER: Dynamics error (Tue Feb 08 2005 - 08:09:04 CST)
  • AMBER: Dynamics error (Tue Feb 08 2005 - 05:25:07 CST)
  • AMBER: dynamics error (Tue Feb 08 2005 - 05:10:19 CST)
  • AMBER:Hydroxy Proline (Thu Jan 20 2005 - 03:19:42 CST)
• s0344557_at_sms.ed.ac.uk
  • Re: AMBER: restart coordinate file (Thu Nov 10 2005 - 10:11:49 CST)
  • AMBER: restart coordinate file (Thu Nov 10 2005 - 07:55:43 CST)
  • AMBER: Dipolar coupling refinement (Fri Oct 21 2005 - 08:04:39 CDT)
• Sagar D Khare
  • AMBER: writing MASKs (Fri Apr 22 2005 - 09:58:24 CDT)
  • AMBER: No. of Snapshots in MM/GB/SA (Tue Apr 12 2005 - 12:48:44 CDT)
• Sagar S. Rane
  • AMBER: antechamber charge methods (Mon Nov 28 2005 - 10:20:45 CST)
• Sagarika Dev
  • AMBER: Parameter for alpha-lactose (Wed May 11 2005 - 09:48:21 CDT)
• Sam
  • Re: AMBER: ambpdb TER problems (Wed Dec 28 2005 - 11:17:14 CST)
  • Re: AMBER: ambpdb TER problems (Tue Dec 27 2005 - 10:23:39 CST)
  • AMBER: ambpdb TER problems (Fri Dec 23 2005 - 10:23:26 CST)
• Sam Moors
  • AMBER: Nose-Hoover thermostat (Thu Apr 21 2005 - 07:40:44 CDT)
• samuel.arey_at_epfl.ch
  • Re: AMBER:how to deal with metal ion? (Fri Dec 30 2005 - 05:05:39 CST)
  • Re: AMBER:how to deal with metal ion? (Fri Dec 30 2005 - 04:56:08 CST)
  • Re: AMBER: ambpdb TER problems (Mon Dec 26 2005 - 13:26:27 CST)
• Sanghyun Park
  • AMBER: Re: inconsistent ordering in an improper dihedral of TRP (Thu Mar 10 2005 - 21:08:25 CST)
  • AMBER: inconsistent ordering in an improper dihedral of TRP (Sun Feb 06 2005 - 22:38:03 CST)
• sanjeev_at_mbu.iisc.ernet.in
  • Re: AMBER: MD: Water network analysis + visualization (Tue Mar 22 2005 - 07:58:24 CST)
• santanu chatterjee
  • AMBER: AMBER topology file format (Mon Aug 22 2005 - 04:18:18 CDT)
• scopio
  • Re: AMBER: radius parameter for F atom (Mon Apr 25 2005 - 20:36:16 CDT)
  • Re: AMBER: Warnings as a file (Mon Apr 11 2005 - 00:03:39 CDT)
  • Re: AMBER: ptraj (Fri Mar 11 2005 - 23:44:04 CST)
  • Re: AMBER: A problem about removing waters and counterions by ptraj (Mon Mar 07 2005 - 07:48:40 CST)
  • AMBER: A problem about removing waters and counterions by ptraj (Mon Mar 07 2005 - 06:28:19 CST)
  • AMBER: minimizing structures before MM-PBSA? (Tue Feb 22 2005 - 19:23:37 CST)
  • Re: AMBER: ptraj problem (Tue Feb 22 2005 - 04:08:28 CST)
  • AMBER: some question about MM-PBSA (Thu Jan 20 2005 - 09:10:39 CST)
  • Re: AMBER: SO4 prep file (Tue Jan 18 2005 - 06:57:29 CST)
• Scott Brozell
  • Re: AMBER: problem with ssh and xleap (Wed Dec 28 2005 - 16:02:48 CST)
  • RE: AMBER: fedora installation problem (Wed Nov 02 2005 - 21:35:16 CST)
  • Re: AMBER: AMBER tests (x86-64, PGI / Intel) (Thu Oct 27 2005 - 19:42:37 CDT)
  • Re: AMBER: Amber8 compilation error (Fri Sep 09 2005 - 01:55:23 CDT)
  • Re: AMBER: crashing xleap; bugfix.44 (Mon May 23 2005 - 12:22:51 CDT)
  • Re: AMBER: crashing xleap (Fri May 20 2005 - 15:03:40 CDT)
  • Re: AMBER: leap single precision (Fri Apr 08 2005 - 02:07:31 CDT)
  • Re: AMBER: Xleap execution problems on Solaris (Tue Mar 01 2005 - 21:36:56 CST)
  • Re: AMBER: problems with running sander in parallel on linux (Tue Feb 15 2005 - 16:02:56 CST)
  • Re: AMBER: problems with running sander in parallel on linux (Tue Feb 15 2005 - 15:01:21 CST)
  • Re: AMBER: problems with running sander in parallel on linux (Tue Feb 15 2005 - 13:42:45 CST)
• Scott E. Boesch
  • AMBER: the restart of replica exchange method (REM) simulations in AMBER8 (Fri Apr 15 2005 - 16:24:24 CDT)
• Scott Pendley
  • Re: AMBER: MM_PBSA problem (Fri Nov 04 2005 - 12:18:17 CST)
  • Re: AMBER: mm_pbsa problem (Tue Nov 01 2005 - 16:36:48 CST)
  • Re: AMBER: Can GB and MS work correctly together in mmpbsa? (Mon Jul 18 2005 - 12:31:29 CDT)
  • Re: AMBER: Can GB and MS work correctly together in mmpbsa? (Fri Jul 15 2005 - 15:08:43 CDT)
  • Re: AMBER: Can GB and MS work correctly together in mmpbsa? (Fri Jul 15 2005 - 12:46:46 CDT)
  • Re: AMBER: Ptraj and order of operations (Tue Jul 12 2005 - 18:22:29 CDT)
  • Re: AMBER: MM_PBSA help, please (Tue Jul 12 2005 - 16:57:08 CDT)
  • Re: AMBER: MM_PBSA help, please (Mon Jul 11 2005 - 16:37:50 CDT)
  • Re: AMBER: MM_PBSA help, please (Mon Jul 11 2005 - 13:30:34 CDT)
  • Re: AMBER: MM-PBSA calculation (Wed Jun 01 2005 - 18:44:05 CDT)
  • Re: AMBER: radius parameter for F atom (Tue May 10 2005 - 14:49:21 CDT)
  • Re: AMBER: mm/pbsa error (Tue May 10 2005 - 14:56:52 CDT)
  • Re: AMBER: radius parameter for F atom (Tue May 10 2005 - 14:49:21 CDT)
  • AMBER: PDB conversion to gzmat using antechamber (Tue Feb 15 2005 - 17:32:21 CST)
• Sebastian Fernandez Alberti
  • AMBER: H-bond energy (Thu Sep 01 2005 - 08:16:14 CDT)
• sebnem
  • Re: AMBER: difference of energy in sander and nmode in amber 7 (Wed Aug 17 2005 - 12:51:15 CDT)
  • Re: AMBER: difference of energy in sander and nmode in amber 7 (Wed Aug 17 2005 - 10:39:02 CDT)
  • AMBER: difference of energy in sander and nmode in amber 7 (Mon Aug 15 2005 - 16:55:24 CDT)
  • AMBER: IDIEL in sander (Fri Mar 11 2005 - 01:14:50 CST)
• Sergey Krishtal
  • AMBER: Amber crashes at simulation in the NVT ensemble with the periodic box equiilbrated in the NPT ensemble. (Thu Dec 22 2005 - 00:15:14 CST)
  • Re[2]: AMBER: AMBER compilation with -DREM (Wed Nov 30 2005 - 05:38:17 CST)
  • AMBER: AMBER compilation with -DREM (Tue Nov 29 2005 - 06:45:46 CST)
• Sergio E. Wong
  • Re: AMBER: troubleshooting replica exchange (Wed Oct 12 2005 - 19:48:45 CDT)
  • AMBER: NRESPA (Sat Aug 27 2005 - 14:12:29 CDT)
  • AMBER: amber 8 REM possible test problem (Tue May 17 2005 - 16:51:04 CDT)
  • AMBER: keeping two domains closed together during a simulation (Thu May 05 2005 - 19:44:45 CDT)
  • Re: AMBER: atommask error (Fri Apr 29 2005 - 12:19:25 CDT)
  • AMBER: atommask error (Fri Apr 29 2005 - 01:02:05 CDT)
  • AMBER: REM mdinfo file (Mon Mar 28 2005 - 19:51:45 CST)
  • Re: AMBER: amber 8 benchmarks dec alpha (Mon Jan 24 2005 - 17:54:41 CST)
  • AMBER: amber 8 benchmarks dec alpha (Mon Jan 24 2005 - 16:08:14 CST)
  • Re: AMBER: problem runing parallel (REM) on tru64 (Sat Jan 22 2005 - 14:44:23 CST)
  • AMBER: problem runing parallel (REM) on tru64 (Fri Jan 21 2005 - 18:22:26 CST)
• Shan Jufang
  • Re: RE: AMBER: about radius of Br in MMPBSA calculation (Wed Sep 21 2005 - 10:05:54 CDT)
  • RE: AMBER: about radius of Br in MMPBSA calculation (Thu Sep 15 2005 - 17:00:56 CDT)
  • RE: Re: AMBER: (Sat Jul 09 2005 - 14:37:54 CDT)
• Shekter, Lee
  • AMBER: Dual Xeon EM64T Intel Fortran Compiler (Mon Apr 18 2005 - 13:17:58 CDT)
  • RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem (Wed Mar 23 2005 - 10:29:57 CST)
  • RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem (Mon Mar 21 2005 - 21:39:42 CST)
  • AMBER: Dual Xeon EM64T Intel Fortran Compile Problem (Mon Mar 21 2005 - 18:12:26 CST)
• Shishir
  • Re: AMBER: amber file formats. (Thu Oct 20 2005 - 15:37:16 CDT)
  • AMBER: amber file formats. (Wed Oct 19 2005 - 15:16:04 CDT)
• shuli
  • Re: AMBER: All the tests passed except prmtop and prepin... (Mon Apr 04 2005 - 09:56:23 CDT)
  • Re: AMBER: All the tests passed except prmtop and prepin... (Sun Apr 03 2005 - 10:24:47 CDT)
• shuli kang
  • Re: AMBER: What does a crash mean while running a md simulation? (Tue Jan 25 2005 - 01:35:45 CST)
  • Re: AMBER: What does a crash mean while running a md simulation? (Mon Jan 24 2005 - 23:58:54 CST)
  • AMBER: What does a crash mean while running a md simulation? (Sun Jan 23 2005 - 23:56:00 CST)
• Shulin Zhuang
  • Re: AMBER: Is the MD simulation normal (Thu Jun 30 2005 - 09:52:03 CDT)
  • Re: AMBER: Is the MD simulation normal (Thu Jun 30 2005 - 10:00:11 CDT)
  • Re: AMBER: Is the MD simulation normal (Wed Jun 29 2005 - 10:03:20 CDT)
  • Re: AMBER: Is the MD simulation normal (Wed Jun 29 2005 - 05:11:53 CDT)
  • Re: AMBER: antechamber problems (Mon Jun 20 2005 - 20:07:56 CDT)
  • Re: AMBER: Need help in charge fitting through RESP (Mon Jun 13 2005 - 09:29:02 CDT)
  • Re: AMBER: density problem (Tue May 31 2005 - 20:49:47 CDT)
  • Re: AMBER: Error on restrained MD equilibration (AMBER 7) (Tue May 31 2005 - 20:36:32 CDT)
  • Re: AMBER: Is the MD simulation normal (Mon May 30 2005 - 09:39:50 CDT)
  • Re: AMBER: Is the MD simulation normal (Sun May 29 2005 - 09:53:35 CDT)
  • Re: AMBER: Is the MD simulation normal (Sat May 28 2005 - 08:02:05 CDT)
  • Re: AMBER: Is the MD simulation normal (Fri May 27 2005 - 02:38:05 CDT)
  • Re: AMBER: Is the MD simulation normal (Thu May 26 2005 - 23:23:37 CDT)
  • AMBER: Is the MD simulation normal (Thu May 26 2005 - 10:30:48 CDT)
  • Re: AMBER: antechamber not working .. for thio residue.. (Sun May 22 2005 - 21:31:27 CDT)
  • Re: AMBER: Re: antechamber not working .. for thio residue.. (Fri May 20 2005 - 05:22:39 CDT)
  • Re: AMBER: How to create a parallel job for amber 8? (Sat May 14 2005 - 08:45:54 CDT)
  • Re: AMBER: the restraint MD fail with amber8,but success with amber7 (Fri May 13 2005 - 06:21:28 CDT)
  • Re: AMBER: the restraint MD fail with amber8,but success with amber7 (Fri May 13 2005 - 06:19:20 CDT)
  • AMBER: the restraint MD fail with amber8,but success with amber7 (Thu May 12 2005 - 20:44:04 CDT)
• Shuting Wei
  • AMBER: Cluster analysis by MMTSB or ptraj (Fri Oct 28 2005 - 10:30:49 CDT)
• Sichun Yang
  • AMBER: increase the limit of restraintmask (Thu Dec 22 2005 - 12:58:14 CST)
  • Re: AMBER: Free energy pertubation (thermodynamic intergration) (Mon Apr 25 2005 - 11:55:16 CDT)
  • AMBER: carnal - water-mediated HBond (Fri Jan 21 2005 - 16:36:52 CST)
• Simon Whitehead
  • AMBER: ptraj crash error (Fri Dec 02 2005 - 11:51:47 CST)
  • AMBER: ifort compiling problem (Wed Nov 30 2005 - 09:27:48 CST)
  • AMBER: fedora installation problem (Wed Nov 02 2005 - 10:11:26 CST)
  • AMBER: improper torsion parameters (Tue Sep 13 2005 - 12:23:13 CDT)
  • AMBER: fixing protein for minimisation of solvent (Sat Sep 03 2005 - 05:56:55 CDT)
  • AMBER: ptraj correlation facility (Fri Aug 19 2005 - 04:15:41 CDT)
  • AMBER: (Thu Jun 02 2005 - 07:44:03 CDT)
  • AMBER: Which forcefield? (Tue May 24 2005 - 03:13:01 CDT)
  • AMBER: Using amber4 generated prep files in amber8? (Thu May 19 2005 - 07:51:00 CDT)
• snowyowls
  • AMBER:how to deal with metal ion? (Fri Dec 30 2005 - 00:24:58 CST)
  • Re: AMBER: a quistion about compile (Fri Dec 23 2005 - 06:32:52 CST)
  • Re: AMBER: a quistion about compile (Wed Dec 21 2005 - 08:53:21 CST)
  • Re: AMBER: a quistion about compile (Tue Dec 20 2005 - 07:30:07 CST)
• Soo
  • AMBER: AMBER8 crashes machine(nodes) under IBM compiler, Suse Linux, amd IBM loadleveler (Sun Jul 31 2005 - 21:45:01 CDT)
  • AMBER: GB solvation and "boxed" environment simulation (Thu Feb 17 2005 - 23:32:38 CST)
  • AMBER: Is droplet boundary condition option possible ? (Sat Feb 05 2005 - 00:18:36 CST)
• Soo Joo
  • AMBER: Amber8 installation on IBM (power4) with SUSE 9.1 Linux (IBM XLF compiler) (Tue Apr 19 2005 - 04:36:26 CDT)
• Spero Manolatos
  • RE: AMBER: parameter for sulfur in thio-octyl-glucopyranoside (Thu May 12 2005 - 17:08:49 CDT)
• Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
  • Re: AMBER: fail of minimization in sander (Wed Jun 15 2005 - 06:05:25 CDT)
  • Re: AMBER: Protein ions? (Thu Jun 02 2005 - 09:57:02 CDT)
  • Re: AMBER: question about initial conditions for amber (Mon May 30 2005 - 06:40:59 CDT)
  • AMBER: interaction between residues (Wed Apr 20 2005 - 09:27:31 CDT)
  • AMBER: doble C and N terminal (Tue Apr 05 2005 - 04:45:58 CDT)
  • AMBER: GBSA calculation (Mon Feb 28 2005 - 04:59:23 CST)
  • Re: AMBER: Cyclic peptide (Wed Feb 16 2005 - 03:48:19 CST)
• Stefano Federico Pieraccini
  • Re: AMBER: question about initial conditions for amber (Mon May 30 2005 - 06:44:54 CDT)
• Stefano.Pieraccini_at_unimi.it
  • Re: AMBER: Atom type :Si (Fri Jul 22 2005 - 03:37:50 CDT)
• Stephen P. Molnar, Ph.D.
  • AMBER: Compiling Amber7 wint Intel Fortran v8 Compiler (Tue Jul 19 2005 - 15:14:30 CDT)
  • AMBER: Amber 7 Compiler Error (Tue Jul 19 2005 - 07:26:14 CDT)
• Stern, Julie
  • AMBER: nucgen H5T H3T (Mon Jul 25 2005 - 20:55:52 CDT)
  • AMBER: nucgen bdna types (Fri Jul 22 2005 - 20:01:20 CDT)
  • AMBER: infinite DNA (Fri Jul 08 2005 - 16:44:25 CDT)
  • AMBER: SOURCE3 in gaff.dat (Fri Jun 10 2005 - 04:40:20 CDT)
  • AMBER: eelnb (Mon Jun 06 2005 - 15:16:31 CDT)
  • AMBER: double counting of potentials (Tue May 31 2005 - 18:04:43 CDT)
  • AMBER: 1-4 scaling factors (Fri May 20 2005 - 14:13:22 CDT)
  • AMBER: output of force field info (Mon May 16 2005 - 14:24:37 CDT)
  • RE: AMBER: SANDER BOMB: volume of ucell too big (Thu May 12 2005 - 14:34:55 CDT)
  • AMBER: SANDER BOMB: volume of ucell too big (Wed May 11 2005 - 11:07:38 CDT)
  • AMBER: false bond created upon coordinate retrieval (Thu Apr 28 2005 - 16:29:38 CDT)
  • AMBER: ibelly not working (Wed Apr 20 2005 - 14:40:28 CDT)
  • AMBER: periodic boundaries and repeating structure (Thu Apr 14 2005 - 12:55:09 CDT)
  • AMBER: vdw or center box dimensions, periodicity, and the jagged edge (Tue Apr 12 2005 - 12:30:38 CDT)
  • AMBER: ibelly not working (Tue Apr 12 2005 - 11:52:56 CDT)
  • AMBER: breaking symmetry in minimization (Mon Apr 11 2005 - 15:58:53 CDT)
  • AMBER: leap bond error (Thu Mar 31 2005 - 19:11:29 CST)
  • AMBER: tleap,xleap bond order for triple bonds (Tue Mar 29 2005 - 16:49:38 CST)
  • AMBER: periodicity problem (Wed Mar 16 2005 - 15:02:28 CST)
  • AMBER: in vacuo parameters (Tue Mar 15 2005 - 17:14:44 CST)
  • AMBER: setBox buffer in leap (Fri Feb 25 2005 - 12:43:19 CST)
  • Re: AMBER: lastrst (Wed Feb 23 2005 - 15:03:57 CST)
  • AMBER: lastrst (Tue Feb 22 2005 - 19:21:00 CST)
  • AMBER: lastrst (Tue Feb 22 2005 - 17:06:24 CST)
  • AMBER: vlimit exceeded and temperature blow up (Tue Feb 22 2005 - 10:36:05 CST)
  • AMBER: molecule blowing apart during equilibration (Fri Feb 18 2005 - 01:12:16 CST)
  • AMBER: leap saveamberparm chain types response (Thu Feb 17 2005 - 17:16:50 CST)
  • AMBER: EWALD and belly not strictly correct (Tue Feb 15 2005 - 23:41:49 CST)
  • AMBER: desc NEWRES and blank unit type (Wed Feb 09 2005 - 20:07:00 CST)
  • AMBER: leap bond angle building (Tue Feb 08 2005 - 17:44:39 CST)
  • AMBER: trajectory of minimization (Fri Feb 04 2005 - 17:49:17 CST)
  • AMBER: huge bond distances in new residue (Fri Feb 04 2005 - 17:48:14 CST)
  • AMBER: protonate and input conversion error (Thu Feb 03 2005 - 10:48:20 CST)
  • AMBER: xleap MOVE and .lib file (Wed Feb 02 2005 - 11:01:55 CST)
  • AMBER: gold atoms (Tue Jan 25 2005 - 10:53:09 CST)
  • AMBER: test suite possible failures (Mon Jan 24 2005 - 13:39:42 CST)
  • AMBER: amber 8 installation (Fri Jan 21 2005 - 11:28:17 CST)
• Steve Seibold
  • AMBER: Position restraints and Models (Thu Dec 01 2005 - 14:54:06 CST)
  • RE: AMBER: Xleap menu bar problems (Mon Sep 19 2005 - 15:44:52 CDT)
  • AMBER: Xleap menu bar problems (Mon Sep 19 2005 - 14:29:09 CDT)
  • AMBER: (Fri May 20 2005 - 12:45:24 CDT)
  • AMBER: Moil-view and Quicktime movie (Thu Apr 21 2005 - 09:55:01 CDT)
  • AMBER: Trajectory problems (Thu Mar 17 2005 - 15:44:23 CST)
  • AMBER: Trajectory problems (Thu Mar 17 2005 - 13:21:37 CST)
• Stuart Murdock
  • AMBER: Topology Format Amber 8 (Tue Feb 15 2005 - 06:00:56 CST)
• Sukjoon Yoon
  • AMBER: Error message (Mon Nov 14 2005 - 02:14:07 CST)
  • AMBER: AMBER compilation error (Thu Oct 06 2005 - 21:32:36 CDT)
  • AMBER: AMBER compilation - RH Enterprise 4, Xeon EM64T (Wed Oct 05 2005 - 00:55:07 CDT)
  • AMBER: Installation error - icc: command not found (Tue Oct 04 2005 - 20:13:11 CDT)
  • AMBER: RESTARTED DUE TO LINMIN FAILURE (Sat Jul 30 2005 - 01:00:24 CDT)
  • AMBER: Protein residue numbering (Wed Jul 27 2005 - 06:52:42 CDT)
  • AMBER: Installation problem. . (Thu Jun 16 2005 - 09:49:19 CDT)
  • AMBER: Installation problem. . (Wed Jun 15 2005 - 01:08:51 CDT)
  • AMBER: Installation problem (Sun Jun 12 2005 - 23:07:26 CDT)
  • RE: AMBER: Installation problem (Sun Jun 12 2005 - 21:35:37 CDT)
  • AMBER: Installation problem (Sun Jun 12 2005 - 04:21:50 CDT)
• support_at_skyfi.com
  • Important Information About Your Sky Bank Account (Mon Sep 05 2005 - 11:32:11 CDT)
• Suxin Zheng
  • Re: AMBER: Ligand problem (Mon Dec 19 2005 - 19:05:13 CST)
  • AMBER: Can I get each corresponding sanpshots' delta delta energy term from mm_pbsa (Mon Sep 12 2005 - 17:43:13 CDT)
  • Re: AMBER: How is the origin of the grid defined?(PBSA question) (Tue Aug 16 2005 - 15:54:27 CDT)
  • Re: AMBER: mm_pbsa (Fri Jul 29 2005 - 19:39:15 CDT)
  • AMBER: pbsa problem (Wed Jul 27 2005 - 14:47:29 CDT)
  • AMBER: mmpbsa test problem (Fri Jul 22 2005 - 20:41:11 CDT)
  • AMBER: Have the parameters for dUMP been calculated by somebody? (Fri Jun 24 2005 - 20:30:12 CDT)
  • Re: AMBER: Parameters for phosphorylated amino acids (Thu Jun 23 2005 - 17:41:30 CDT)
  • AMBER: Compile Problems of Parallel Amber8 on Mac G5 (Wed Jun 08 2005 - 18:02:23 CDT)
• Svetlana Kirillova
  • Re: AMBER: nonbonded interactions (Wed Mar 23 2005 - 03:23:47 CST)
  • AMBER: nonbonded interaction (Tue Mar 22 2005 - 10:37:54 CST)
• sychen
  • Re[2]: AMBER: What does a crash mean while running a md simulation? (Tue Dec 06 2005 - 06:16:49 CST)
  • Re: AMBER: Fluorine in MM-PBSA (AMBER8) (Wed Nov 30 2005 - 23:43:55 CST)
  • Re[2]: AMBER: Force field modification problem (Mon May 30 2005 - 19:05:45 CDT)
• Sébastien Fiorucci
  • AMBER: ANAL problem (Mon Nov 21 2005 - 11:18:07 CST)
  • AMBER: Neutral C-terminal residue (Wed Oct 19 2005 - 05:12:44 CDT)
• Takashi Nakamura
  • AMBER: H-atom types attached to a carbon atom next to carbonyl group (Mon Jan 17 2005 - 11:52:56 CST)
• tanc_at_uci.edu
  • AMBER: Question about NVE simulation. (Tue Oct 18 2005 - 00:45:51 CDT)
  • AMBER: "ERROR TERMINATION DUE TO SHAKE OR TORCON" in Gibbs (Tue Mar 22 2005 - 23:11:41 CST)
  • AMBER: Question about TI integral method (Sun Jan 23 2005 - 04:01:33 CST)
• Tatyana B Mamonova
  • AMBER: ptraj analysis (Mon Mar 28 2005 - 11:24:55 CST)
• thanyarat Udom
  • AMBER: Why I couldnt used carnal for analyzed RMSD ? (Wed Feb 16 2005 - 03:28:17 CST)
  • AMBER: How to converts a binary mdcrd file (Fri Feb 11 2005 - 02:00:10 CST)
  • AMBER: How to converts a binary mdcrd file (Fri Feb 11 2005 - 01:02:21 CST)
• thenmalar
  • AMBER: tleap and water (Wed Apr 20 2005 - 03:13:58 CDT)
• Thomas Cheatham
  • Re: AMBER: (no subject) (Fri Dec 23 2005 - 15:37:57 CST)
  • Re: AMBER: lib-4324 : UNRECOVERABLE library error (Wed Dec 21 2005 - 21:16:22 CST)
  • Re: AMBER: How to add water to calculate MMPBSA. . (Thu Dec 15 2005 - 12:09:47 CST)
  • Re: AMBER: RMSD Calculations (Mon Dec 05 2005 - 16:50:36 CST)
  • Re: AMBER: Mg2+ issues of using MM-PB/GBSA (Thu Dec 01 2005 - 23:27:21 CST)
  • Re: AMBER: My model loses its motion in MD (Thu Nov 24 2005 - 10:03:07 CST)
  • Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? (Tue Nov 22 2005 - 22:35:11 CST)
  • Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? (Mon Nov 21 2005 - 21:50:09 CST)
  • Re: AMBER: average struct without solvent (Mon Nov 21 2005 - 10:34:23 CST)
  • Re: AMBER: ptraj Hbond analysis (Sun Nov 20 2005 - 17:13:44 CST)
  • Re: AMBER: ptraj Hbond analysis (Thu Nov 17 2005 - 23:20:00 CST)
  • Re: AMBER: need clarification on EWALD BOMB error (Thu Nov 17 2005 - 11:45:28 CST)
  • Re: AMBER: ptraj Hbond analysis (Wed Nov 16 2005 - 23:28:42 CST)
  • Re: AMBER: Quantifying DNA perterbation (Tue Nov 15 2005 - 23:55:55 CST)
  • Re: AMBER: ptraj hbond analysis (Thu Oct 20 2005 - 21:03:36 CDT)
  • Re: AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue (Thu Oct 20 2005 - 20:50:43 CDT)
• Thomas E. Cheatham, III
  • Re: AMBER: MD problems/shake (Tue Dec 20 2005 - 13:20:26 CST)
  • Re: AMBER: MD problems/shake (Mon Dec 19 2005 - 17:40:40 CST)
  • Re: AMBER: MD problems/shake (Mon Dec 19 2005 - 14:53:40 CST)
  • Re: AMBER: ptraj distance mask (Wed Nov 02 2005 - 11:32:09 CST)
  • Re: AMBER: MM_PB/GBSA (Thu Sep 29 2005 - 23:04:46 CDT)
  • Re: AMBER: Trajectory Problem (Tue Sep 27 2005 - 11:59:50 CDT)
  • Re: AMBER: D-enantiomers (Tue Sep 20 2005 - 21:36:34 CDT)
  • Re: AMBER: about the %occupied of hydrogen bond (Fri Sep 16 2005 - 09:30:58 CDT)
  • Re: AMBER: Error in "restrt" output file (Wed Sep 14 2005 - 16:41:41 CDT)
  • Re: AMBER: ptraj problem (Thu Sep 01 2005 - 15:54:24 CDT)
  • Re: AMBER: Why are some of the Lennard-Jones coeffs 0 ? (Wed Aug 31 2005 - 12:53:38 CDT)
  • Re: AMBER: group-based cutoff (Wed Aug 10 2005 - 21:53:38 CDT)
  • Re: AMBER: ptraj command inputs (Wed Aug 10 2005 - 17:43:31 CDT)
  • Re: AMBER: ptraj help, how to enable disabled ptraj routine? (Mon Aug 01 2005 - 15:51:27 CDT)
  • Re: AMBER: Minimized structure (Thu Jul 28 2005 - 22:09:55 CDT)
  • Re: AMBER: nucgen error (U not generated) (Wed Jul 27 2005 - 22:49:33 CDT)
  • Re: AMBER: Minimized structure (Wed Jul 27 2005 - 22:47:28 CDT)
  • Re: AMBER: convert_trajectory (Wed Jul 27 2005 - 18:45:34 CDT)
  • Re: AMBER: convert_trajectory (Wed Jul 27 2005 - 16:27:57 CDT)
  • Re: AMBER: Periodic box imaging using ptraj (Tue Jul 26 2005 - 15:11:39 CDT)
  • Re: AMBER: ptraj-acceptor mask format (Tue Jul 26 2005 - 15:06:08 CDT)
  • AMBER: Re: Problems with ptraj/rdparm (Fri Jul 15 2005 - 14:22:28 CDT)
  • Re: AMBER: example script for hbond calculation (Fri Jul 01 2005 - 11:10:07 CDT)
  • Re: AMBER: Is the MD simulation normal (Thu May 26 2005 - 12:41:03 CDT)
  • Re: AMBER: hbond analysis in ptaj/carnal (Thu May 26 2005 - 12:05:00 CDT)
  • Re: AMBER: Error: vlimit exceeded for step (Tue May 24 2005 - 13:12:58 CDT)
  • Re: AMBER: 1-4 scaling factors (Fri May 20 2005 - 14:43:34 CDT)
  • Re: AMBER: error during MD run (Wed May 18 2005 - 13:10:36 CDT)
  • Re: AMBER: output of force field info (Mon May 16 2005 - 20:21:51 CDT)
  • Re: AMBER: Asking how to creat alanine "dipeptide" in amber8 (Wed May 11 2005 - 10:38:54 CDT)
  • Re: AMBER: Pyranose pucker parameters (Wed Apr 27 2005 - 22:57:26 CDT)
  • Re: AMBER: Problem when converting AMBER trajectories to CHARMM format (Sat Apr 23 2005 - 18:33:48 CDT)
  • Re: AMBER: intramolecular nonbonded interactions in AMBER force field (Thu Apr 21 2005 - 09:50:24 CDT)
  • Re: AMBER: Non-Bonded Cutoff vs PME (Wed Apr 20 2005 - 09:53:38 CDT)
  • Re: AMBER: tleap and water (Wed Apr 20 2005 - 09:28:33 CDT)
  • Re: AMBER: Non-Bonded Cutoff vs PME (Tue Apr 19 2005 - 18:47:10 CDT)
  • Re: AMBER: big fluctuation in MM-PBSA/GA (Thu Apr 14 2005 - 18:53:48 CDT)
  • Re: AMBER: small target pressure in constant pressure dynamics (Thu Apr 14 2005 - 17:09:18 CDT)
  • Re: AMBER: Fail to load the trajectory file. (Mon Apr 11 2005 - 21:08:11 CDT)
  • Re: AMBER: Re:Re:single-stranded poly(rC) simulation (Tue Apr 05 2005 - 13:32:15 CDT)
  • Re: AMBER: trajectory alignment using ptraj (Fri Apr 01 2005 - 15:38:50 CST)
  • Re: AMBER: trajectory alignment using ptraj (Fri Apr 01 2005 - 14:39:07 CST)
  • Re: AMBER: trajectory alignment using ptraj (Fri Apr 01 2005 - 11:47:30 CST)
  • Re: AMBER: PTRAJ:"hbond" analysis (Wed Mar 30 2005 - 11:40:16 CST)
  • Re: AMBER: align snapshots to a reference (Wed Mar 30 2005 - 10:23:21 CST)
  • Re: AMBER: Minimization of avg structure-SANDER Bomb (Thu Mar 17 2005 - 13:01:33 CST)
  • Re: AMBER: Hydrogen bonding question (Tue Mar 15 2005 - 09:59:00 CST)
  • Re: Re :AMBER: Holes in water (Sat Mar 12 2005 - 16:20:32 CST)
  • Re: AMBER: how can I deal with the puzzle? (Tue Mar 08 2005 - 21:53:48 CST)
  • Re: AMBER: Restraint of atoms during minimization (Tue Feb 22 2005 - 11:36:42 CST)
  • Re: AMBER: MPI for sander8 (Tue Feb 22 2005 - 11:22:18 CST)
  • Re: AMBER: problem with ptraj and randomizeions (Thu Feb 17 2005 - 12:57:23 CST)
  • Re: AMBER: sander segmentation fault (Wed Feb 02 2005 - 17:59:13 CST)
  • Re: AMBER: Problem in ptraj (Wed Feb 02 2005 - 12:34:01 CST)
  • Re: AMBER: Suspended (tty input) (Thu Jan 20 2005 - 18:09:16 CST)
  • AMBER: ptraj analysis (Wed Jan 19 2005 - 12:16:17 CST)
  • Re: AMBER: distance between images (Wed Jan 05 2005 - 11:29:19 CST)
• Thomas Patko
  • Re: AMBER: transfer data from Linux to windows (Thu Jun 09 2005 - 17:49:02 CDT)
  • Re: AMBER: AMBER8 Build on Linux x64 running Opterons (Wed May 11 2005 - 10:34:18 CDT)
  • AMBER: AMBER8 Build on Linux x64 running Opterons (Wed May 11 2005 - 02:10:14 CDT)
  • Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) (Wed May 11 2005 - 02:10:53 CDT)
  • Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) (Thu May 05 2005 - 17:02:40 CDT)
  • AMBER: Bromelain PDF xleap load error (Wed May 04 2005 - 12:13:35 CDT)
  • Re: AMBER: X Windows for LEaP on SGI (Tue Mar 08 2005 - 23:44:26 CST)
  • AMBER: AMBER8 Compile Error on Dual Opteron (Sun Mar 06 2005 - 19:53:46 CST)
• Thomas Steinbrecher
  • AMBER: Simulating transition metals in amber (Thu Oct 20 2005 - 04:32:58 CDT)
  • Re: AMBER: Mg2+ radius in my_parse_delphi.siz (Tue Sep 27 2005 - 01:49:05 CDT)
  • Re: AMBER: Free energy calculation for protein-protein complex using MM_PBSA (Thu Jun 30 2005 - 02:14:01 CDT)
  • Re: AMBER: radius parameter for Mg2+ in mm_pbsa calculation (Mon Jun 06 2005 - 02:23:16 CDT)
  • Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth (Tue Apr 26 2005 - 03:37:01 CDT)
  • Re: AMBER: Dummy Atom Types on both states (Tue Feb 15 2005 - 03:04:06 CST)
• Thomas Whitington
  • Re: AMBER: mm_pbsa example number 3 (Sat Sep 10 2005 - 21:32:58 CDT)
  • AMBER: mm_pbsa example number 3 (Fri Sep 09 2005 - 03:14:19 CDT)
• Tim Meyer
  • Re: AMBER:how to deal with metal ion? (Fri Dec 30 2005 - 10:09:07 CST)
  • Re: AMBER:how to deal with metal ion? (Fri Dec 30 2005 - 10:05:06 CST)
  • Re: AMBER: An atom name with 4 characters is not compatible with Leap ? (Fri Jul 22 2005 - 10:06:52 CDT)
  • AMBER: rdparm (Tue Apr 12 2005 - 09:23:55 CDT)
  • Re: AMBER: Protein with structural ions (Thu Apr 07 2005 - 09:05:15 CDT)
  • Re: AMBER: surface area (Mon Apr 04 2005 - 10:38:12 CDT)
• Tiziano Tuccinardi
  • AMBER: MM_PBSA question (Thu Nov 24 2005 - 03:01:53 CST)
  • Re: AMBER: compiling pmemd on dual xeon (Tue May 17 2005 - 13:05:49 CDT)
  • AMBER: compiling pmemd on dual xeon (Tue May 17 2005 - 12:28:31 CDT)
• tomjas
  • Re: AMBER: XRED II error while initializing (Wed Nov 09 2005 - 00:38:40 CST)
• tomjas_at_poczta.onet.pl
  • AMBER: XRED II error while initializing (Mon Nov 07 2005 - 06:17:12 CST)
  • Re: Re: AMBER: An error during minimization using RED (Wed Mar 02 2005 - 07:18:00 CST)
  • Re: Re: AMBER: An error during minimization using RED (Wed Mar 02 2005 - 03:15:15 CST)
  • AMBER: An error during minimization using RED (Tue Mar 01 2005 - 01:18:55 CST)
• tonglei
  • Re: AMBER: temprature and restraint in constant volumm MD (Mon Nov 21 2005 - 07:56:12 CST)
  • AMBER: temprature and restraint in constant volumm MD (Mon Nov 21 2005 - 02:55:40 CST)
• Toshifumi Yui
  • Re: AMBER: antechamber dimesion size, again (Thu Oct 06 2005 - 21:14:47 CDT)
  • AMBER: antechamber dimesion size, again (Thu Oct 06 2005 - 04:44:29 CDT)
  • AMBER: Making prep file of sugar derivative (Thu Sep 29 2005 - 07:02:12 CDT)
  • AMBER: AMBER antechamber; dimenion size (Tue Sep 06 2005 - 22:22:17 CDT)
• tpatko
  • AMBER: Re: AMBER Test Error (Follow Up) (Sun Apr 24 2005 - 19:55:18 CDT)
  • AMBER: AMBER Test Error (Sun Apr 24 2005 - 19:31:42 CDT)
• Troy Wymore
  • AMBER: PSC Summer Workshop: Modeling Proteins and Nucleic Acids with AMBER, VMD and the MMTSB Toolkit (Thu Feb 17 2005 - 13:00:36 CST)
• Tru Huynh
  • Re: AMBER: compile amber8 on RHEL4 (Fri Feb 25 2005 - 07:09:33 CST)
• Ulf Ryde
  • AMBER: highly fluctuating reaction field energies in MM/PBSA (Thu Sep 22 2005 - 05:32:05 CDT)
• vannajan_at_chiangmai.ac.th
  • AMBER: bond breaking/ energetic ion (Tue Aug 02 2005 - 21:11:16 CDT)
• Varsha Goyal
  • Re: AMBER: About Salt concentration (Fri Dec 16 2005 - 19:37:45 CST)
  • AMBER: About Salt concentration (Fri Dec 16 2005 - 18:03:05 CST)
  • Re: AMBER: Making movie from AMBER trajectory (Mon Nov 07 2005 - 12:13:09 CST)
  • Re: AMBER: Making movie from AMBER trajectory (Mon Nov 07 2005 - 11:23:50 CST)
  • RE: AMBER: Making movie from AMBER trajectory (Mon Nov 07 2005 - 11:25:41 CST)
  • AMBER: Making movie from AMBER trajectory (Mon Nov 07 2005 - 10:03:01 CST)
  • RE: AMBER: Could not open file (Melb.mdcrd) with mode (r) (Tue Sep 20 2005 - 16:25:45 CDT)
  • AMBER: Could not open file (Melb.mdcrd) with mode (r) (Mon Sep 19 2005 - 11:50:42 CDT)
  • AMBER: random-coil polymer (Sat Jul 16 2005 - 17:35:19 CDT)
  • AMBER: AMBER on Mac OS X (Wed Jul 06 2005 - 09:55:12 CDT)
  • Re: AMBER: (no subject) (Sat Jul 02 2005 - 11:10:49 CDT)
  • AMBER: (no subject) (Fri Jul 01 2005 - 16:46:55 CDT)
  • Re: AMBER: Analysing my simulation data.. (Sat Jun 18 2005 - 11:21:28 CDT)
  • AMBER: Question about tutorial-9 (Tue Jun 07 2005 - 11:27:57 CDT)
• Venkata S Koppuravuri
  • AMBER: NAN errors (Tue Jan 25 2005 - 15:39:45 CST)
• Vidana.Epa_at_csiro.au
  • AMBER: re Updating Tutorials (Thu Mar 17 2005 - 21:17:50 CST)
• Vijay Manickam Achari
  • AMBER: molecular dynamics (Sat Jul 09 2005 - 21:55:55 CDT)
  • AMBER: question about leaprc.gaff and xxx.top (Fri Jul 01 2005 - 00:52:15 CDT)
  • AMBER: example script for hbond calculation (Thu Jun 30 2005 - 01:27:15 CDT)
  • AMBER: acceptor and donor in hbond calculation (Thu Jun 30 2005 - 00:01:58 CDT)
  • AMBER: calculating hydrogen bonds (Tue Jun 28 2005 - 21:50:36 CDT)
  • AMBER: calculating torsion angles (Tue Jun 28 2005 - 03:59:02 CDT)
  • AMBER: script for calculating hydrogen bond (Mon Jun 27 2005 - 21:57:30 CDT)
  • AMBER: using xmgrace.... (Thu Jun 23 2005 - 21:51:37 CDT)
  • AMBER: Analysing my simulation data.. (Sat Jun 18 2005 - 03:32:13 CDT)
  • AMBER: creating pdb file.... (Tue Jun 14 2005 - 05:49:09 CDT)
  • Re: AMBER: how to pull out frames (Mon Jun 13 2005 - 23:04:42 CDT)
  • AMBER: how to pull out frames (Mon Jun 13 2005 - 00:23:51 CDT)
  • Re: AMBER: dissolving micelle structure in water.. amber7 (Thu May 26 2005 - 20:19:57 CDT)
  • AMBER: dissolving micelle structure in water.. amber7 (Wed May 25 2005 - 22:59:22 CDT)
  • AMBER: my prepin file in lowe-case (Tue May 24 2005 - 02:51:55 CDT)
  • AMBER: my frcmod file created using parmchk (Mon May 23 2005 - 22:44:21 CDT)
  • AMBER: how to generate frcmod file for using prepin file.. (Mon May 23 2005 - 21:52:18 CDT)
  • AMBER: using antechamber ... to get prepin file (Mon May 23 2005 - 03:59:16 CDT)
  • AMBER: antechamber not working .. for thio residue.. (Sun May 22 2005 - 21:15:20 CDT)
  • AMBER: how to creat leaprc.gaff (Fri May 20 2005 - 04:36:25 CDT)
  • AMBER: Re: antechamber not working .. for thio residue.. (Fri May 20 2005 - 04:32:19 CDT)
  • AMBER: the out put I get... parameter for sulfur in thio-glucoside residue (Thu May 19 2005 - 01:55:21 CDT)
  • AMBER: parameter for sulfur in thio-glucoside residue (Wed May 18 2005 - 20:58:57 CDT)
  • AMBER: parameter for sulfur in thio-octyl-glucopyranoside (Mon May 09 2005 - 22:23:07 CDT)
• Viktor Hornak
  • Re: AMBER: error about using ambmask (Thu Dec 08 2005 - 07:53:22 CST)
  • Re: AMBER: Targeted MD (Wed Nov 30 2005 - 11:46:55 CST)
  • Re: AMBER: using position restraints in target MD? (Fri Oct 21 2005 - 15:14:42 CDT)
  • Re: AMBER: atommask question (Fri Sep 23 2005 - 11:46:39 CDT)
  • Re: AMBER: setting up restraint with ntr option (Thu Jun 09 2005 - 18:53:05 CDT)
  • Re: AMBER: Error on restrained MD equilibration (AMBER 7) (Tue May 31 2005 - 10:52:48 CDT)
  • Re: AMBER: question about TGMD: vlimit exceeded for step (Fri Apr 08 2005 - 17:24:13 CDT)
  • Re: AMBER: question about TGMD: vlimit exceeded for step (Fri Apr 08 2005 - 15:47:40 CDT)
  • Re: AMBER: force constant Unit used in TMD (Mon Apr 04 2005 - 11:53:23 CDT)
  • Re: AMBER: TMD force constant (Tue Mar 22 2005 - 07:42:37 CST)
  • Re: AMBER: Replica Exchange crashing (Fri Mar 18 2005 - 06:51:48 CST)
  • Re: AMBER: restraintmask dimension (Wed Mar 16 2005 - 07:46:27 CST)
  • Re: AMBER: Sander error (Fri Mar 11 2005 - 10:36:38 CST)
  • Re: AMBER: MPI for sander8 (Tue Feb 22 2005 - 11:13:46 CST)
  • Re: AMBER: sander errors with atom restraints on ia64 (Thu Feb 17 2005 - 16:46:26 CST)
  • Re: AMBER: AMBER 8: Freeze AND restrain questions (Mon Jan 24 2005 - 12:02:53 CST)
• Vineet Pande
  • RE: AMBER: using antechamber ... to get prepin file (Mon May 23 2005 - 07:02:26 CDT)
  • Re: AMBER: No vdW parameters for HO.. (Fri May 06 2005 - 10:40:09 CDT)
  • AMBER: No vdW parameters for HO.. (Fri May 06 2005 - 05:20:02 CDT)
  • Re: AMBER: How can I read parm99.dat file? (Thu May 05 2005 - 04:12:09 CDT)
  • RE: AMBER: writing MASKs (Fri Apr 22 2005 - 10:45:43 CDT)
  • Re: AMBER: intramolecular nonbonded interactions in AMBER force field (Thu Apr 21 2005 - 08:26:30 CDT)
  • Re: AMBER: intramolecular nonbonded interactions in AMBER force field (Thu Apr 21 2005 - 03:33:19 CDT)
  • Re: AMBER: Non-Bonded Cutoff vs PME (Wed Apr 20 2005 - 04:17:20 CDT)
  • AMBER: Non-Bonded Cutoff vs PME (Tue Apr 19 2005 - 11:13:26 CDT)
  • RE: AMBER: About Gaussian Key Words (Thu Apr 07 2005 - 03:36:04 CDT)
  • Re: AMBER: PTRAJ:"hbond" analysis (Thu Mar 31 2005 - 03:17:57 CST)
  • AMBER: PTRAJ:"hbond" analysis (Wed Mar 30 2005 - 11:15:30 CST)
  • RE: AMBER: Parameter files for general lipids (Tue Mar 29 2005 - 01:28:48 CST)
  • AMBER: PTRAJ:"hbond" doubts (Sun Mar 27 2005 - 07:55:24 CST)
  • RE: AMBER: question about placing a substrate in a protein pocket (Fri Mar 25 2005 - 03:41:18 CST)
  • RE: AMBER: Could not open file (trajin) with mode (r) (Wed Mar 23 2005 - 10:26:06 CST)
  • RE: AMBER: ANAL module/AMBER8 (Tue Mar 22 2005 - 12:11:22 CST)
  • AMBER: ANAL module/AMBER8 (Tue Mar 22 2005 - 11:32:06 CST)
  • Re: AMBER: Minimization of avg structure-SANDER Bomb (Thu Mar 17 2005 - 14:11:10 CST)
  • Re: AMBER: Minimization of avg structure-SANDER Bomb (Thu Mar 17 2005 - 12:45:01 CST)
  • AMBER: Minimization of avg structure-SANDER Bomb (Thu Mar 17 2005 - 08:50:03 CST)
  • AMBER: van der Waals interactions (PTRAJ) (Thu Mar 17 2005 - 08:07:12 CST)
  • RE: AMBER: question about amber parameter file format etc. (Wed Mar 16 2005 - 12:06:53 CST)
  • Re: AMBER: Velocity Info (Wed Mar 16 2005 - 10:02:04 CST)
  • AMBER: Velocity Info (Wed Mar 16 2005 - 08:08:42 CST)
  • RE: AMBER: Problems Binding Protein to DNA (Wed Mar 09 2005 - 05:16:44 CST)
  • RE: AMBER: How to build dynamics input for guanine with tleap ? (Thu Feb 24 2005 - 08:35:23 CST)
  • RE: AMBER: classes (Thu Feb 24 2005 - 08:29:19 CST)
  • RE: AMBER: constrains (Mon Feb 14 2005 - 09:48:39 CST)
  • RE: AMBER:how to analyse trajectory files (Mon Feb 14 2005 - 05:07:21 CST)
  • RE: AMBER: stereo (Wed Feb 09 2005 - 12:51:06 CST)
  • RE: AMBER: minimize a ptraj average pdb structure (Wed Feb 09 2005 - 04:05:14 CST)
  • AMBER: ANTECHAMBER & DIVCON (Wed Jan 26 2005 - 04:18:17 CST)
  • RE: AMBER: How to make PDB file by myself (Tue Jan 25 2005 - 05:06:42 CST)
  • RE: AMBER: eedmeth=5 (Sun Jan 23 2005 - 05:46:23 CST)
  • RE: AMBER: H-atom types attached to a carbon atom next to carbonyl group (Mon Jan 17 2005 - 14:32:37 CST)
  • RE: AMBER: Coordinate Superimposition in PTRAJ (Mon Jan 17 2005 - 03:45:20 CST)
  • AMBER: Coordinate Superimposition in PTRAJ (Sun Jan 16 2005 - 05:42:09 CST)
  • RE: FW: AMBER: parametrization problem (Sat Jan 15 2005 - 05:15:39 CST)
• Vitor Manuel Sousa F?x
  • Re: AMBER: Minimized structure (Thu Jul 28 2005 - 06:07:09 CDT)
  • AMBER: PMF calculations with TI using the sander (Mon Jul 18 2005 - 02:30:59 CDT)
  • AMBER: MMPBSA calculations on Highly charged systems (Tue May 17 2005 - 06:01:21 CDT)
• Vlad Cojocaru
  • AMBER: no thermostat versus very weak thermostat (Thu Dec 01 2005 - 09:57:15 CST)
  • AMBER: MD without a thermostat (Thu Dec 01 2005 - 09:32:57 CST)
  • AMBER: constant pressure vs. constant volume heating (Tue Nov 29 2005 - 12:50:39 CST)
  • AMBER: reordering atoms after antechamber (Fri Nov 25 2005 - 11:02:38 CST)
  • AMBER: GRID program used to add ions and solvate AMBER minimized structures (Tue Nov 22 2005 - 08:53:55 CST)
  • Re: AMBER: RED: extra variable definition (Tue Nov 22 2005 - 08:26:49 CST)
  • AMBER: Leap handling crystallographic waters (Tue Nov 22 2005 - 07:44:57 CST)
  • Re: AMBER: RED: extra variable definition (Tue Nov 22 2005 - 03:08:32 CST)
  • AMBER: RED: extra variable definition (Sun Nov 20 2005 - 08:48:32 CST)
  • AMBER: RED&GAMESS: sorry ... my mistake (Fri Nov 18 2005 - 06:28:31 CST)
  • AMBER: RED and EP from GAMESS (Fri Nov 18 2005 - 04:12:49 CST)
  • AMBER: Leap task (Fri Nov 04 2005 - 05:44:39 CST)
  • AMBER: Leap error: Could not find atom type: CE (Wed Nov 02 2005 - 12:08:33 CST)
  • AMBER: problem with xleap (Tue Oct 18 2005 - 08:56:38 CDT)
  • AMBER: units describing projection onto modes (Thu Feb 24 2005 - 12:40:18 CST)
  • AMBER: correlation along PCA modes (Mon Feb 07 2005 - 05:35:44 CST)
  • AMBER: Carnal in Amber8 (Tue Feb 01 2005 - 10:11:09 CST)
  • AMBER: plane definition in ptraj (Fri Jan 28 2005 - 12:00:23 CST)
  • AMBER: pucker: deatails about pucker calculation (Fri Jan 28 2005 - 09:13:13 CST)
  • AMBER: sugar pucker with Carnal and ptraj (Fri Jan 28 2005 - 08:56:23 CST)
  • AMBER: calculating electrostatic potential (Tue Jan 25 2005 - 04:59:48 CST)
  • AMBER: enhanced sampling methods (Wed Jan 19 2005 - 12:13:58 CST)
  • AMBER: last call for early registrations for "Horizons2005" (Fri Jan 14 2005 - 07:19:00 CST)
• Vojtìch Klusák
  • AMBER: Sander error (Thu Mar 10 2005 - 06:03:21 CST)
  • AMBER: amber 8 problem (Mon Jan 31 2005 - 07:01:35 CST)
  • AMBER: FW: amber 8 problem (Mon Jan 24 2005 - 02:13:47 CST)
• Wai Keat Yam
  • RE: AMBER: pdb file and xleap (Thu Jul 21 2005 - 01:01:07 CDT)
  • AMBER: pdb file and xleap (Tue Jul 19 2005 - 05:06:50 CDT)
  • AMBER: substitute missing residues? (Fri Jun 10 2005 - 03:20:29 CDT)
  • Re: AMBER: R.E.D (Sun Mar 06 2005 - 20:31:57 CST)
  • AMBER: R.E.D (Sat Mar 05 2005 - 23:14:49 CST)
• Wei Chen
  • Re: AMBER: MM_PBSA_parameter (Wed Nov 23 2005 - 16:51:16 CST)
  • AMBER: MM_PBSA_parameter (Wed Nov 23 2005 - 13:48:12 CST)
  • Re: AMBER: MM/PBSA basic questions (Fri Nov 18 2005 - 11:06:04 CST)
  • Re: AMBER: Question about using MM_PBSA (Thu Nov 17 2005 - 17:50:05 CST)
  • Re: AMBER: mm_pbsa (Mon Nov 14 2005 - 16:06:44 CST)
  • Re: AMBER: mm_pbsa (Sat Nov 12 2005 - 22:45:14 CST)
  • Re: AMBER: mm_pbsa (Fri Nov 11 2005 - 11:21:32 CST)
  • Re: AMBER: mm_pbsa (Fri Nov 11 2005 - 11:05:40 CST)
  • AMBER: mm_pbsa (Wed Nov 09 2005 - 13:51:01 CST)
  • Re: AMBER: Ask for helpf to get examples for MM-PBSA with AMBER8 (Thu Nov 03 2005 - 14:07:25 CST)
  • Re: AMBER: solvation energy (Wed Sep 07 2005 - 11:19:47 CDT)
  • Re: AMBER: glycan (Wed Aug 17 2005 - 17:29:52 CDT)
  • Re: AMBER: Energy Comparisons (Wed Aug 17 2005 - 17:24:08 CDT)
  • AMBER: glycan (Wed Aug 17 2005 - 13:25:27 CDT)
  • RE: AMBER: nmode (Thu Aug 04 2005 - 22:07:43 CDT)
  • AMBER: nmode (Thu Aug 04 2005 - 13:04:17 CDT)
  • RE: AMBER: memory_mm_pbsa (Mon Aug 01 2005 - 23:03:34 CDT)
  • AMBER: memory_mm_pbsa (Mon Aug 01 2005 - 22:00:34 CDT)
  • Re: AMBER: mm_pbsa (Fri Jul 29 2005 - 22:53:36 CDT)
  • Re: AMBER: mm_pbsa (Fri Jul 29 2005 - 20:09:13 CDT)
  • Re: AMBER: mm_pbsa (Fri Jul 29 2005 - 19:55:07 CDT)
  • AMBER: mm_pbsa (Fri Jul 29 2005 - 19:10:46 CDT)
  • Re: AMBER: convert_trajectory (Wed Jul 27 2005 - 21:06:28 CDT)
  • Re: AMBER: convert_trajectory (Wed Jul 27 2005 - 18:07:55 CDT)
  • AMBER: convert_trajectory (Wed Jul 27 2005 - 15:58:36 CDT)
• Wei Wang
  • AMBER: parameter meaning (Fri Mar 18 2005 - 12:33:15 CST)
• Wei Zhang
  • Re: AMBER: a quistion about compile (Tue Dec 20 2005 - 10:35:34 CST)
  • Re: AMBER: a quistion about compile (Mon Dec 19 2005 - 11:01:22 CST)
  • Re: AMBER: some problems with Antechamber (Tue Nov 29 2005 - 11:14:53 CST)
  • Re: AMBER: rounding in xleap when using saveoff command... (Wed Nov 02 2005 - 13:34:10 CST)
  • Re: AMBER: REMD error!!! (Thu Oct 20 2005 - 11:15:51 CDT)
  • Re: AMBER: Trajectory Problem (Tue Sep 27 2005 - 11:40:45 CDT)
  • Re: AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters (Tue Apr 05 2005 - 02:49:38 CDT)
  • Re: AMBER: A few question about RDF input preparation (Thu Mar 24 2005 - 05:58:47 CST)
  • Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' (Wed Mar 23 2005 - 18:49:14 CST)
  • Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' (Tue Mar 22 2005 - 19:34:26 CST)
  • Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' (Tue Mar 22 2005 - 18:29:26 CST)
  • Re: AMBER: Amber8 Parallel installation troubles (Tue Mar 22 2005 - 17:39:06 CST)
• Wells, David H
  • RE: Re: AMBER: (Tue Apr 05 2005 - 02:13:56 CDT)
  • AMBER: igb10 vlimit exceeded (Thu Mar 31 2005 - 03:08:55 CST)
  • Re: AMBER: igb=10 some vdW terms disappear? (Wed Mar 23 2005 - 12:40:53 CST)
  • AMBER: igb=10 some vdW terms disappear? (Mon Mar 21 2005 - 01:54:23 CST)
• Wen Li
  • Re: AMBER: trajectory alignment using ptraj (Fri Apr 01 2005 - 20:42:43 CST)
  • Re: AMBER: trajectory alignment using ptraj (Fri Apr 01 2005 - 15:37:57 CST)
  • Re: AMBER: trajectory alignment using ptraj (Fri Apr 01 2005 - 15:23:14 CST)
  • Re: AMBER: trajectory alignment using ptraj (Fri Apr 01 2005 - 14:12:34 CST)
  • Re: AMBER: trajectory alignment using ptraj (Fri Apr 01 2005 - 12:42:36 CST)
  • AMBER: trajectory alignment using ptraj (Fri Apr 01 2005 - 11:38:02 CST)
  • Re: AMBER: align snapshots to a reference (Wed Mar 30 2005 - 13:52:34 CST)
  • Re: AMBER: align snapshots to a reference (Wed Mar 30 2005 - 10:14:44 CST)
  • Re: AMBER: align snapshots to a reference (Wed Mar 30 2005 - 09:43:21 CST)
  • AMBER: align snapshots to a reference (Tue Mar 29 2005 - 15:38:36 CST)
• wendy
  • Re: AMBER: fail of minimization in sander (Thu Jun 16 2005 - 21:43:11 CDT)
  • Re: AMBER: fail of minimization in sander (Thu Jun 16 2005 - 03:19:15 CDT)
  • Re: AMBER: fail of minimization in sander (Wed Jun 15 2005 - 02:54:59 CDT)
  • Re: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 11:13:10 CDT)
  • Re: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 10:57:08 CDT)
  • Re: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 05:06:01 CDT)
  • Re: AMBER: fail of minimization in sander (Sun Jun 05 2005 - 23:59:15 CDT)
  • AMBER: fail of minimization in sander (Sun Jun 05 2005 - 22:01:25 CDT)
• wenfei Li
  • AMBER: broblem of replica exchange MD with polarizable force field (Wed Aug 31 2005 - 19:51:32 CDT)
  • Re: AMBER: NTWPRY problem (Mon Jul 25 2005 - 20:51:09 CDT)
  • Re: AMBER: NTWPRY problem (Mon Jul 25 2005 - 20:42:16 CDT)
  • Re: AMBER: NTWPRY problem (Mon Jul 25 2005 - 20:39:21 CDT)
  • AMBER: NTWPRY problem (Mon Jul 25 2005 - 10:44:31 CDT)
• Whitney Allen
  • AMBER: Targeted MD (Wed Nov 30 2005 - 10:20:10 CST)
  • AMBER: tRNA's modified bases in the Amber parameters database (Mon Nov 07 2005 - 08:52:45 CST)
  • RE: AMBER: xleap with modified residue (Mon Oct 24 2005 - 11:24:25 CDT)
  • AMBER: xleap with modified residue (Thu Oct 20 2005 - 13:12:42 CDT)
  • AMBER: Targeted MD (Thu Oct 20 2005 - 13:04:31 CDT)
  • AMBER: Antechamber error "Cannot successfully assign bond type for this molecule" (Thu Aug 25 2005 - 11:13:11 CDT)
• Woojin Lee
  • AMBER: Question about partial charge for ligand molecules (Wed Dec 28 2005 - 20:37:47 CST)
  • AMBER: xleap: different distance results from "check" command in xleap (Tue Feb 01 2005 - 23:54:14 CST)
• Wu Yingliang
  • Re: Re: AMBER: On the role of neutralizing ions in GB-MD and GBSA (Thu Apr 21 2005 - 21:50:09 CDT)
  • AMBER: On the role of neutralizing ions in GB-MD and GBSA (Thu Apr 21 2005 - 05:16:29 CDT)
  • AMBER: On the role of neutralizing ions in GB-MD and GBSA (Thu Apr 21 2005 - 05:26:05 CDT)
  • AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters (Tue Apr 05 2005 - 01:18:11 CDT)
• wulei
  • AMBER: Is AMBER package suitable for simulating multiple molecule in solvent? (Wed Oct 05 2005 - 04:26:00 CDT)
• Xavier Deupi
  • AMBER: local dielectric constant (Mon Apr 18 2005 - 20:17:40 CDT)
• xhu1_at_memphis.edu
  • AMBER: software for real polymer MD simulation (Wed Jun 22 2005 - 16:31:51 CDT)
  • Re: AMBER: question about TGMD: vlimit exceeded for step (Fri Apr 08 2005 - 18:04:17 CDT)
  • Re: AMBER: question about TGMD: vlimit exceeded for step (Fri Apr 08 2005 - 16:55:05 CDT)
  • AMBER: question about TGMD: vlimit exceeded for step (Fri Apr 08 2005 - 15:31:10 CDT)
  • Re: AMBER: force constant Unit used in TMD (Mon Apr 04 2005 - 12:59:02 CDT)
  • Re: AMBER: force constant Unit used in TMD (Mon Apr 04 2005 - 12:28:36 CDT)
  • Re: AMBER: force constant Unit used in TMD (Mon Apr 04 2005 - 11:33:01 CDT)
  • AMBER: force constant Unit used in TMD (Mon Apr 04 2005 - 10:05:30 CDT)
  • AMBER: reference of Targeted MD (Fri Apr 01 2005 - 15:52:59 CST)
  • Re: AMBER: radii "leap" from which file (Tue Mar 08 2005 - 21:06:22 CST)
  • AMBER: radii "leap" from which file (Tue Mar 08 2005 - 13:34:48 CST)
• Xiao He
  • Re: Re: AMBER: Sander: idecomp (Mon Mar 28 2005 - 07:44:53 CST)
  • AMBER: ico(i)=-1? (Fri Feb 25 2005 - 21:49:46 CST)
• xiaoqin huang
  • AMBER: Re: restraints (Wed Oct 26 2005 - 16:25:03 CDT)
  • Re: AMBER: QMMM question (Mon Oct 10 2005 - 13:59:55 CDT)
  • AMBER: QMMM question (Thu Oct 06 2005 - 23:09:53 CDT)
• Xiaoqing Wang
  • AMBER: How to set AMBER parameter files for lipid? (Sun Jan 16 2005 - 19:38:49 CST)
• Xiaoqing,Wang
  • AMBER: lipid parameter file (Wed Jan 05 2005 - 02:23:07 CST)
  • AMBER: lipid bilayer membrane force field parameter (Tue Jan 04 2005 - 03:51:47 CST)
• Xiaowei (David) Li
  • AMBER: error with ptraj (Tue May 17 2005 - 23:27:33 CDT)
  • AMBER: dppsv returns error code: 29 (Fri Feb 04 2005 - 11:58:56 CST)
  • AMBER: the DNA conformation after engery minimization using NMODE (Mon Jan 10 2005 - 13:32:26 CST)
• xiaowen
  • Re: AMBER: tleap load pdb file (Wed Feb 09 2005 - 12:51:44 CST)
  • RE: AMBER: tleap load pdb file (Mon Feb 07 2005 - 21:52:36 CST)
  • RE: AMBER: tleap load pdb file (Mon Feb 07 2005 - 14:58:39 CST)
  • Re: AMBER: tleap load pdb file (Sat Feb 05 2005 - 11:20:12 CST)
  • AMBER: tleap load pdb file (Fri Feb 04 2005 - 15:18:09 CST)
  • AMBER: tleap load pdb file (Fri Feb 04 2005 - 09:44:17 CST)
  • AMBER: question about tleap load pdb file (Wed Feb 02 2005 - 21:19:19 CST)
  • AMBER: question about xwin load pdb file (Fri Jan 28 2005 - 10:48:28 CST)
  • AMBER: question about xwin load pdb file (Thu Jan 27 2005 - 23:04:57 CST)
  • AMBER: about install amber8 on windows (Thu Jan 06 2005 - 16:56:53 CST)
• Xin Hu
  • AMBER: How to split LES trajectory using TRAJ (Thu Sep 22 2005 - 10:12:51 CDT)
  • Re: AMBER: How to split LES trajectory using TRAJ (Mon Sep 19 2005 - 15:49:47 CDT)
  • AMBER: How to split LES trajectory using TRAJ (Tue Sep 13 2005 - 10:03:20 CDT)
  • AMBER: PBSA error: PB bomb in pd_aaradi (Wed Jun 22 2005 - 09:34:13 CDT)
  • AMBER: pairwise energy decomposition using MM-PBSA (Sun May 29 2005 - 22:38:30 CDT)
  • AMBER: How to restart MM_PBSA or doing the statistics only (Tue Apr 26 2005 - 11:00:05 CDT)
  • Re: AMBER: a problem with mm_pbsa (Tue Apr 19 2005 - 09:44:35 CDT)
  • Re: AMBER: amber8/antechamber installation problem (Tue Apr 19 2005 - 09:14:41 CDT)
  • AMBER: amber8/antechamber installation problem (Sat Apr 16 2005 - 20:39:07 CDT)
  • Re: AMBER: big fluctuation in MM-PBSA/GA (Fri Apr 15 2005 - 15:53:02 CDT)
  • Re: AMBER: big fluctuation in MM-PBSA/GA (Fri Apr 15 2005 - 13:17:28 CDT)
  • Re: AMBER: MM_PBSA problem (Wed Apr 13 2005 - 12:49:05 CDT)
  • Re: AMBER: MM_PBSA problem (Wed Apr 13 2005 - 10:28:17 CDT)
  • Re: AMBER: MM_PBSA problem (Tue Apr 12 2005 - 14:36:07 CDT)
  • Re: AMBER: MM_PBSA problem (Tue Apr 12 2005 - 14:31:45 CDT)
  • AMBER: MM_PBSA problem (Tue Apr 12 2005 - 11:09:36 CDT)
  • Re: AMBER: MM_PBSA error (Mon Apr 11 2005 - 17:33:51 CDT)
  • AMBER: MM_PBSA error (Mon Apr 11 2005 - 13:46:30 CDT)
  • AMBER: across-correlation in ptraj (Wed Mar 02 2005 - 10:20:09 CST)
  • AMBER: cross-correlation (Thu Feb 24 2005 - 10:40:54 CST)
• Xin Wang
  • Re: AMBER: sander segmentation fault (Wed Feb 02 2005 - 15:36:25 CST)
  • AMBER: sander segmentation fault (Tue Feb 01 2005 - 16:15:12 CST)
• xinhuang_at_indiana.edu
  • AMBER: questions about RNA (Mon Jun 27 2005 - 22:19:58 CDT)
• Xioling Chuang
  • AMBER: MM_PBSA stopped at some snapshot (Mon Nov 28 2005 - 23:57:54 CST)
  • AMBER: input for mm_pbsa (Sun Nov 27 2005 - 00:31:09 CST)
  • AMBER: How to wrap a truncated octahedron water box into the primary box? (Sat Nov 26 2005 - 04:19:44 CST)
  • AMBER: Will Amber 9 available? (Sun Nov 20 2005 - 19:54:55 CST)
• Xuebin Qiao
  • Re: AMBER: error with compiling amber8 with lam on intel pc clusters (Thu Dec 15 2005 - 01:57:24 CST)
  • Re: AMBER: error in safe (Mon Oct 24 2005 - 10:26:41 CDT)
  • Re: AMBER: compiling amber with pgi 5.2.4 (Mon Oct 24 2005 - 10:20:08 CDT)
  • Re: AMBER: GNU Autotool integration for Amber8! (Thu Oct 20 2005 - 08:55:10 CDT)
  • Re: AMBER: GNU Autotool integration for Amber8! (Wed Oct 19 2005 - 10:17:54 CDT)
• xueping
  • AMBER: about salt bridges (Fri Aug 05 2005 - 01:34:18 CDT)
  • AMBER: Hbond analysis (Sun Jun 26 2005 - 20:27:48 CDT)
  • Re: AMBER: average structure-ptraj (Sun Apr 10 2005 - 04:10:55 CDT)
  • Re: AMBER: average structure-ptraj (Sun Apr 10 2005 - 03:50:19 CDT)
  • AMBER: average structure-ptraj (Sat Apr 09 2005 - 03:23:23 CDT)
  • Re: AMBER: combine mdcrd using ptraj (Thu Apr 07 2005 - 04:13:59 CDT)
  • Re: AMBER: combine mdcrd using ptraj (Thu Apr 07 2005 - 01:59:54 CDT)
  • AMBER: combine mdcrd using ptraj (Wed Apr 06 2005 - 23:41:48 CDT)
  • AMBER: missing residue (Mon Mar 28 2005 - 01:34:17 CST)
  • Re: AMBER: ptraj (Sat Mar 12 2005 - 01:08:37 CST)
  • AMBER: ptraj (Fri Mar 11 2005 - 22:56:29 CST)
• Y. Xu
  • Re: Re: AMBER: Protein with structural ions (Fri Apr 08 2005 - 01:39:45 CDT)
  • AMBER: makeDIST_RST ERROR (Thu Apr 07 2005 - 21:14:19 CDT)
• Yagi Toru
  • AMBER: The effect appling paches (Tue Apr 19 2005 - 08:11:54 CDT)
• Yam
  • Re: AMBER: aniso and iso (Mon Dec 19 2005 - 02:17:43 CST)
  • AMBER: aniso and iso (Thu Dec 15 2005 - 04:11:45 CST)
  • Re: AMBER: ew_legal.h (Tue Nov 15 2005 - 01:10:18 CST)
  • RE: AMBER: ew_legal.h (Mon Nov 14 2005 - 22:40:37 CST)
  • AMBER: ew_legal.h (Mon Nov 14 2005 - 20:54:03 CST)
  • Re: AMBER: (no subject) (Thu Oct 20 2005 - 02:31:37 CDT)
  • AMBER: sander error (Mon Oct 17 2005 - 21:10:50 CDT)
  • RE: AMBER: sander error (Tue Oct 11 2005 - 04:21:08 CDT)
  • AMBER: sander error (Sun Oct 09 2005 - 21:04:20 CDT)
  • AMBER: in vacuo? (Tue Aug 30 2005 - 04:53:07 CDT)
  • Re: AMBER: Tutorial question and some more... (Wed Aug 10 2005 - 02:50:54 CDT)
  • Re: AMBER: Minimized structure (Thu Jul 28 2005 - 23:03:40 CDT)
  • Re: AMBER: Minimized structure (Thu Jul 28 2005 - 21:25:29 CDT)
  • AMBER: Minimized structure (Wed Jul 27 2005 - 22:02:03 CDT)
• Yanze Zhang
  • AMBER: MD on surface (Tue May 17 2005 - 18:58:29 CDT)
  • Re: AMBER: Re: R.E.D. question (Mon May 02 2005 - 14:19:14 CDT)
  • AMBER: building helix bundle (Thu Mar 17 2005 - 15:30:54 CST)
  • AMBER: A problem about Gaussian (Thu Mar 03 2005 - 16:38:59 CST)
  • AMBER: gaussian output file (Mon Jan 31 2005 - 11:09:40 CST)
  • AMBER: antechamber error message (Thu Jan 27 2005 - 09:02:46 CST)
• Ye Mei
  • AMBER: No skew or curtosis when zero variance in moment (Wed Dec 21 2005 - 09:56:43 CST)
  • AMBER: error with compiling amber8 with lam on intel pc clusters (Wed Dec 14 2005 - 21:36:54 CST)
  • Re: Re: AMBER: bug report (Tue Nov 08 2005 - 19:30:35 CST)
  • AMBER: bug report (Sun Nov 06 2005 - 00:21:50 CST)
  • AMBER: parallel amber8 with mpi through qsnet (Thu Aug 18 2005 - 21:11:55 CDT)
  • AMBER: coordinated water molecules deleted when addions (Mon Aug 01 2005 - 04:20:11 CDT)
  • AMBER: dihedral term in prmtop file (Thu Jul 28 2005 - 09:38:55 CDT)
  • AMBER: potential of mean force calculation along reaction coordinates (Tue Jul 26 2005 - 02:04:00 CDT)
  • AMBER: simulation with Mg2+ ions and counter ions (Sat Jul 09 2005 - 01:54:16 CDT)
  • AMBER: how to average the structure along md trajectory (Wed Jul 06 2005 - 08:51:56 CDT)
  • AMBER: estimation of interface size (Sun Jul 03 2005 - 21:19:55 CDT)
  • AMBER: molecular dynamics simulation of protein containing Mg2+ cation (Fri Jul 01 2005 - 04:33:31 CDT)
  • AMBER: least square fit of snapshots in md trajectory to a reference frame (Thu Jun 30 2005 - 21:56:08 CDT)
  • AMBER: large std error in entropy estimation (Tue Jun 21 2005 - 21:51:43 CDT)
  • Re: RE: AMBER: SHAKE in md with partial solvation (Tue Jun 07 2005 - 08:46:49 CDT)
  • AMBER: Re: Re: AMBER: SHAKE in md with partial solvation (Mon Jun 06 2005 - 05:49:44 CDT)
  • Re: AMBER: SHAKE in md with partial solvation (Sun Jun 05 2005 - 06:19:45 CDT)
  • AMBER: SHAKE in md with partial solvation (Sun Jun 05 2005 - 02:30:00 CDT)
  • AMBER: radius parameter for Mg2+ in mm_pbsa calculation (Sat Jun 04 2005 - 09:37:04 CDT)
  • Re: Re: AMBER: radius parameter for F atom (Tue Apr 26 2005 - 08:30:07 CDT)
  • AMBER: radius parameter for F atom (Mon Apr 25 2005 - 12:05:06 CDT)
  • AMBER: coordinates translation (Sun Apr 24 2005 - 11:26:39 CDT)
  • AMBER: a problem with mm_pbsa (Tue Apr 19 2005 - 09:23:01 CDT)
  • AMBER: Does anybody know the experimental solvation free energies of Efavirenz and some other DPC drugs (Tue Apr 12 2005 - 10:19:37 CDT)
  • Re: RE: AMBER: problem with MD simulation (Fri Mar 04 2005 - 19:46:24 CST)
  • AMBER: problem with MD simulation (Tue Mar 01 2005 - 02:00:31 CST)
  • Re: AMBER: compile amber8 on RHEL4 (Fri Feb 25 2005 - 06:01:17 CST)
  • Re: Re: AMBER: separate solvent-solvent and solvent-solute interaction (Mon Feb 21 2005 - 21:21:48 CST)
  • AMBER: separate solvent-solvent and solvent-solute interaction (Mon Feb 21 2005 - 06:44:22 CST)
  • AMBER: simulation with explicit water molecules (Sat Feb 19 2005 - 21:24:48 CST)
• yen li
  • RE: AMBER: Dihedral Energy calculation (Fri Mar 04 2005 - 15:29:08 CST)
  • RE: AMBER: Dihedral Energy calculation (Wed Mar 02 2005 - 12:03:24 CST)
  • RE: AMBER: Dihedral Energy calculation (Wed Mar 02 2005 - 06:37:01 CST)
  • AMBER: Dihedral Energy calculation (Tue Mar 01 2005 - 12:12:56 CST)
  • Re: AMBER: problem with protein minimization (Tue Feb 22 2005 - 03:26:37 CST)
  • AMBER: problem with protein minimization (Mon Feb 21 2005 - 03:12:02 CST)
  • AMBER: (no subject) (Sun Feb 20 2005 - 12:16:32 CST)
  • Re: AMBER: amber8 parallel sander (Mon Jan 17 2005 - 11:55:26 CST)
  • Re: AMBER: amber8 parallel sander (Wed Jan 12 2005 - 07:54:48 CST)
  • AMBER: amber8 parallel sander (Wed Jan 12 2005 - 04:57:19 CST)
• Yen-Ting Lai
  • Re: AMBER: Question about "nmanal" (Tue Jul 12 2005 - 08:36:25 CDT)
  • Re: AMBER: Question about "nmanal" (Tue Jul 12 2005 - 05:09:24 CDT)
  • AMBER: Question about "nmanal" (Mon Jul 11 2005 - 09:11:25 CDT)
  • Re: AMBER: Question about "quasih" (Wed Jun 15 2005 - 14:25:57 CDT)
  • AMBER: Question about "quasih" (Wed Jun 15 2005 - 11:46:22 CDT)
• ygao_at_phase1.unl.edu
  • AMBER: how to solvate in TIP5P box (Wed Jan 26 2005 - 09:59:43 CST)
  • AMBER: Suspended (tty input) (Thu Jan 20 2005 - 17:39:48 CST)
  • RE: AMBER: sander failure (Thu Jan 20 2005 - 16:31:37 CST)
  • RE: AMBER: sander failure (Thu Jan 20 2005 - 16:09:56 CST)
  • AMBER: sander failure (Thu Jan 20 2005 - 15:46:56 CST)
• ying xiong
  • Re: Re: AMBER: rdparm: a parameter array overflowed (Tue Oct 25 2005 - 01:03:27 CDT)
  • AMBER: rdparm: a parameter array overflowed (Mon Oct 24 2005 - 04:17:33 CDT)
  • AMBER: how to get the parameters for modified amino acid residue? (Thu Apr 07 2005 - 22:31:14 CDT)
• yipinl_at_umich.edu
  • Re: AMBER: Dummy Atom Types on both states (Tue Feb 15 2005 - 09:31:56 CST)
  • Re: AMBER: TI with electrostatic decoupling at sander (Thu Jan 27 2005 - 11:39:46 CST)
  • Re: AMBER: TI with electrostatic decoupling at sander (Wed Jan 26 2005 - 11:19:43 CST)
  • AMBER: TI with electrostatic decoupling at sander (Mon Jan 24 2005 - 23:15:43 CST)
• Yogesh Sabnis
  • AMBER: Anal - problems with energy analysis (Tue Jul 12 2005 - 03:33:30 CDT)
  • AMBER: Loading a macmodel file complex (Mon Jul 04 2005 - 10:02:49 CDT)
  • AMBER: Cut pdb files (Thu Jun 16 2005 - 02:57:18 CDT)
• Yong Xu
  • AMBER: amber7.0: F,Br,radius in MMPBSA (Sat Oct 29 2005 - 09:47:21 CDT)
  • AMBER: amber7.0: F,Br,radius in MMPBSA (Sat Oct 29 2005 - 09:46:00 CDT)
  • AMBER: atmtypenumbers (Mon Oct 24 2005 - 22:25:00 CDT)
  • Re: (2) Re: AMBER: F,Cl,Br,I in MMPBSA (Thu Oct 20 2005 - 20:21:33 CDT)
  • Re: Re: AMBER: F,Cl,Br,I in MMPBSA (Thu Oct 20 2005 - 20:12:15 CDT)
  • Re: Re: AMBER: delphi and surface in MMPBSA (Thu Oct 20 2005 - 20:09:07 CDT)
  • AMBER: delphi and surface in MMPBSA (Thu Oct 20 2005 - 09:07:17 CDT)
  • AMBER: again: F, Cl, Br, I in MMPBSA (Fri Oct 14 2005 - 22:07:59 CDT)
  • AMBER: F,Cl,Br,I in MMPBSA (Wed Oct 12 2005 - 03:58:53 CDT)
  • Re: RE: AMBER: about radius of Br in MMPBSA calculation (Fri Sep 16 2005 - 03:41:30 CDT)
  • AMBER: about radius of Br in MMPBSA calculation (Wed Sep 14 2005 - 21:36:35 CDT)
  • Re: AMBER: How to insert a protein in lipid bilayer (Wed Jul 27 2005 - 20:47:22 CDT)
  • AMBER: fit (Mon Jul 25 2005 - 04:04:57 CDT)
  • Re: RE: AMBER: about run time in GB and PB (Thu Apr 21 2005 - 08:17:19 CDT)
  • Re: Re: AMBER: about run time in GB and PB (Thu Apr 21 2005 - 03:55:41 CDT)
  • AMBER: about run time in GB and PB (Thu Apr 21 2005 - 03:06:27 CDT)
  • AMBER: (Tue Apr 19 2005 - 21:57:44 CDT)
  • Re: Re: AMBER: MM-PBSA in protein-Zn-ligand system (Tue Apr 12 2005 - 22:17:00 CDT)
  • AMBER: MM-PBSA in protein-Zn-ligand system (Tue Apr 12 2005 - 20:37:55 CDT)
• Yong Duan
  • RE: AMBER: does the result of H bond is consistent with the ?Eele of MM_PBSA? (Fri Dec 23 2005 - 00:43:53 CST)
  • RE: AMBER: the averaged structure VS the specific snapshot (Fri Dec 23 2005 - 00:38:00 CST)
  • RE: AMBER: Invalid Digit "*" (Wed Sep 28 2005 - 15:50:21 CDT)
  • RE: AMBER: minimization stuck problem (Sat Aug 20 2005 - 08:05:03 CDT)
  • AMBER: RE: is calculated B-factors always smaller than experimental ones? (Mon Aug 08 2005 - 13:24:26 CDT)
  • RE: AMBER: nmode (Thu Aug 04 2005 - 19:03:26 CDT)
  • RE: AMBER: temperature keep increasing in high temp. (Fri Jul 29 2005 - 22:43:52 CDT)
  • RE: AMBER: a bimolecular reaction (Fri Jul 22 2005 - 14:25:09 CDT)
  • Re: AMBER: a bimolecular reaction (Fri Jul 22 2005 - 12:44:23 CDT)
  • Re: AMBER: Protein dynamics. (Wed Jun 08 2005 - 12:24:02 CDT)
  • RE: AMBER: Is the MD simulation normal (Sun May 29 2005 - 11:46:44 CDT)
  • RE: AMBER: Is the MD simulation normal (Fri May 27 2005 - 11:31:27 CDT)
  • RE: AMBER: Is the MD simulation normal (Fri May 27 2005 - 01:17:00 CDT)
  • RE: AMBER: Is the MD simulation normal (Thu May 26 2005 - 12:05:14 CDT)
  • Re: AMBER: No vdW parameters for HO.. (Fri May 06 2005 - 11:28:25 CDT)
  • RE: AMBER: about run time in GB and PB (Thu Apr 21 2005 - 03:57:32 CDT)
  • Large files to AMBER, RE: AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation. (Wed Apr 20 2005 - 10:16:55 CDT)
  • RE: AMBER: small target pressure in constant pressure dynamics (Thu Apr 14 2005 - 18:30:09 CDT)
  • RE: AMBER: a bimolecular reaction (Wed Apr 13 2005 - 14:51:08 CDT)
  • RE: AMBER: freee energy calculation without minimised structure (Wed Apr 13 2005 - 02:40:26 CDT)
  • Re: AMBER: a bimolecular reaction (Tue Apr 12 2005 - 19:22:51 CDT)
• Yong Xu
  • Re: AMBER: about run time in GB and PB (Fri Apr 22 2005 - 03:19:05 CDT)
  • Re: Re: AMBER: Protein with structural ions (Tue Apr 05 2005 - 23:34:55 CDT)
• YoungJin Cho
  • AMBER: E of amber calculations (Wed Dec 14 2005 - 11:34:47 CST)
  • Re: AMBER: Making movie from AMBER trajectory (Tue Nov 08 2005 - 09:00:07 CST)
  • Re: AMBER: R factors in NMR intensity refinement (Thu Oct 06 2005 - 11:56:02 CDT)
  • AMBER: pdb files from traj file (Wed Jul 13 2005 - 16:06:30 CDT)
  • AMBER: sander run (Mon May 02 2005 - 15:45:01 CDT)
  • AMBER: Watson-Crick restraints (Wed Apr 13 2005 - 09:43:22 CDT)
  • Re: AMBER: creating a new residue (Tue Mar 01 2005 - 09:18:16 CST)
  • Re: AMBER: Antechamber/formatting question (Mon Feb 21 2005 - 10:15:32 CST)
• yuann
  • AMBER: Conformational energy (QM) for parameterization (Fri Aug 05 2005 - 05:09:14 CDT)
  • AMBER: Force field modification problem (Mon May 30 2005 - 06:16:27 CDT)
  • AMBER: make test.lmod error (Fri Feb 25 2005 - 10:45:11 CST)
• yuann_at_bioinfo.ndhu.edu.tw
  • AMBER: Fluorine in MM-PBSA (AMBER8) (Wed Nov 30 2005 - 10:30:36 CST)
• Yuqin Cai
  • AMBER: R factors in NMR intensity refinement (Thu Oct 06 2005 - 11:29:31 CDT)
• Yuuki A. Komata
  • AMBER: recompiling problem on IBM aix (Thu Jan 06 2005 - 20:35:46 CST)
• Yuuki Komata
  • Re: AMBER: Citing Generalized Born Implicit solvent Model (igb=5) (Sun Mar 06 2005 - 19:14:18 CST)
  • Re: AMBER: replica exchange trouble with unit 6 (Thu Jan 27 2005 - 19:27:50 CST)
  • AMBER: replica exchange trouble with unit 6 (Thu Jan 27 2005 - 08:39:03 CST)
  • AMBER: mm_pbsa example doesn't run (Fri Jan 21 2005 - 06:10:48 CST)
• zgleo
  • AMBER: Questions about MM-PBSA in Amber8 (Thu Dec 01 2005 - 23:04:26 CST)
  • AMBER: Question of PB bomb (Mon Nov 21 2005 - 22:59:54 CST)
  • AMBER: Question about PB bomb (Mon Nov 21 2005 - 20:11:08 CST)
  • Re: Re: AMBER: mm_pbsa (Sun Jul 31 2005 - 10:26:02 CDT)
  • AMBER: Amber parameters for ADP (Sat Jul 30 2005 - 00:22:19 CDT)
• Zhang Bing
  • AMBER: MM_PBSA problem---Illegal division by zero at ... (Tue Nov 22 2005 - 18:15:40 CST)
  • AMBER: MM_PBSA problem (Tue Nov 22 2005 - 09:37:32 CST)
  • AMBER: MM_PB/GBSA (Thu Sep 29 2005 - 22:13:05 CDT)
  • AMBER: no statistics part (Thu Sep 22 2005 - 10:29:52 CDT)
  • RE: AMBER: Problem finding transition state using NMODE (Thu Sep 22 2005 - 10:27:45 CDT)
  • AMBER: no statistics part (Thu Sep 22 2005 - 10:23:30 CDT)
  • AMBER: ptraj problem (Thu Sep 01 2005 - 02:01:20 CDT)
  • RE: AMBER: installing amber7 on 64bit cluster (Wed Aug 03 2005 - 20:33:55 CDT)
  • AMBER: P4 EM64T Intel Fortran Compile Problem (Wed Jul 20 2005 - 21:24:20 CDT)
  • AMBER: parallel error (Mon Jun 27 2005 - 07:36:14 CDT)
  • AMBER: solutions of amber installation problems (Tue Jun 14 2005 - 21:42:13 CDT)
  • AMBER: Thanks (Tue Jun 14 2005 - 21:26:23 CDT)
  • AMBER: compiler (Tue Jun 14 2005 - 06:13:19 CDT)
  • AMBER: compiler (Tue Jun 14 2005 - 03:14:08 CDT)
  • AMBER: New problem of parallel sander (Thu Jun 02 2005 - 21:46:13 CDT)
  • AMBER: amber8 installation problems (Thu Jun 02 2005 - 01:55:48 CDT)
  • AMBER: amber8 installation problems (Thu Jun 02 2005 - 01:44:47 CDT)
  • AMBER: modeller (Fri May 20 2005 - 23:53:13 CDT)
• Zhang Yingyan
  • AMBER: Using AMBER for Carbon nanotubes (Wed May 18 2005 - 03:21:42 CDT)
• ZhangJian
  • AMBER: For further question about Targeted MD (Wed Mar 09 2005 - 06:48:44 CST)
  • Re: Re: AMBER: how can I deal with the puzzle? (Wed Mar 09 2005 - 01:59:42 CST)
• Zhiguo Liu
  • Re: RE: Re: AMBER: (Sun Jul 10 2005 - 02:37:36 CDT)
  • Re: AMBER: (Sat Jul 09 2005 - 03:39:43 CDT)
  • Re: Re: AMBER: Free energy calculation for protein-protein complex usingMM_PBSA (Thu Jun 30 2005 - 04:56:42 CDT)
  • AMBER: Free energy calculation for protein-protein complex using MM_PBSA (Wed Jun 29 2005 - 20:59:01 CDT)
• zhli_2000
  • AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation. (Wed Apr 20 2005 - 08:52:18 CDT)
• zhli_2000_at_126.com
  • AMBER: some questions about nmode (Tue Dec 20 2005 - 20:30:22 CST)
  • AMBER: nmode error: GNORM is greater than the requested maximum (Wed Dec 14 2005 - 20:16:07 CST)
  • AMBER: error about using ambmask (Thu Dec 08 2005 - 07:40:34 CST)
  • AMBER: The error during calculating PB with pbsa (Sun Dec 04 2005 - 22:39:19 CST)
  • AMBER: Re: (ÈðÐÇÌáʾ-´ËÓʼþ¿ÉÄÜÊÇÀ¬»øÓʼþ)Re: AMBER: Can GB and MS work correctly together in mmpbsa? (Mon Jul 18 2005 - 20:09:23 CDT)
  • AMBER: Re: (ÈðÐÇÌáʾ-´ËÓʼþ¿ÉÄÜÊÇÀ¬»øÓʼþ)Re: AMBER: Can GB and MS work correctly together in mmpbsa? (Mon Jul 18 2005 - 20:23:39 CDT)
  • Re: AMBER: Can GB and MS work correctly together in mmpbsa? (Sat Jul 16 2005 - 22:30:47 CDT)
  • Re: AMBER: Can GB and MS work correctly together in mmpbsa? (Fri Jul 15 2005 - 02:10:41 CDT)
  • AMBER: Can GB and MS work correctly together in mmpbsa? (Thu Jul 14 2005 - 21:38:08 CDT)
  • Re: AMBER: the restarting error (Tue Apr 26 2005 - 05:54:44 CDT)
  • AMBER: the restarting error (Mon Apr 25 2005 - 09:08:02 CDT)
  • AMBER:Bond lengths aren't reasonable after minimisation. (Mon Apr 18 2005 - 05:39:22 CDT)
  • AMBER:FAD can't be minimized. (Mon Apr 11 2005 - 07:48:15 CDT)
• Zhuang
  • AMBER: question convert crd files to pdb files (Tue Nov 29 2005 - 22:02:08 CST)
  • AMBER: troubleshooting replica exchange (Wed Oct 12 2005 - 18:46:08 CDT)
  • AMBER: question temperature coupling tautp value for RNA (Mon Oct 03 2005 - 17:40:09 CDT)
  • AMBER: question temperature coupling tautp value for RNA (Mon Oct 03 2005 - 17:40:23 CDT)
  • Re: AMBER: question replica exchange acceptance ratio (Tue Jul 12 2005 - 17:39:47 CDT)
  • AMBER: question replica exchange acceptance ratio (Tue Jul 12 2005 - 16:01:19 CDT)
• ½¨Æ½ ºú
  • AMBER: TI in Amber8 (Fri Jun 03 2005 - 04:49:02 CDT)
• ÂÀº£æÃ
  • AMBER: Re: Re: AMBER: ATTN REVISION (Mon Apr 18 2005 - 20:38:02 CDT)
  • AMBER: ATTN REVISION (Mon Apr 18 2005 - 03:19:46 CDT)
• ÍõСÇå
  • AMBER: How can i use AMBER with CHARMM forcefield parameter? (Sun Jan 02 2005 - 21:54:25 CST)
• Ò׺ç
  • AMBER: How to create a parallel job for amber 8? (Sat May 14 2005 - 06:20:15 CDT)
• ìÇ Îä
  • AMBER: Two question about dielectric constant (Mon Apr 11 2005 - 03:02:10 CDT)